'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ROpenOffice', 'RODBC'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.2Mb
    po    2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rcplex.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      2.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    include  46.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      3.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.9Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs          12.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      5.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rcrypt.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GOSemSim', 'org.Hs.eg.db'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Note: found 1036 marked UTF-8 strings
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  15.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      5.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Package required and available but unsuitable version: ‘EstimationTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6034 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   [1] 0.075965487837690332   | 0.075965487837690332     [1]            
   [2] 0.080366607041335483   | 0.080366607041335483     [2]            
   [3] 0.116495037965828732   - 0.116495037965828704     [3]            
   [4] 0.094298591805109425   | 0.094298591805109425     [4]            
   [5] 0.056947552169625576   | 0.056947552169625576     [5]            
   [6] 0.059871299449565041   - 0.059871299449565034     [6]            
   [7] 0.113724414671620463   | 0.113724414671620463     [7]            
   [8] 0.090927081012597596   - 0.090927081012597610     [8]            
   [9] 0.103080471397420562   - 0.103080471397420589     [9]            
  [10] 0.055453444393386363   | 0.055453444393386363     [10]           
   ... ...                      ...                      and 10 more ...
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 48 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.6Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  14.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     19.5Mb
    models    1.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Package suggested but not available for checking: ‘ccdata’
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  41.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 272.2Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    libs      264.5Mb
    pictures    1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    doc     1.1Mb
    fonts   1.5Mb
    libs   21.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'showtext', 'sysfonts'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.1/ricu.Rcheck/vign_test/ricu/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See jss.log for more info.
--- failed re-building ‘jss.Rmd’

--- re-building ‘ricu.Rmd’ using rmarkdown
--- finished re-building ‘ricu.Rmd’

--- re-building ‘uom.Rmd’ using rmarkdown
--- finished re-building ‘uom.Rmd’

SUMMARY: processing the following file failed:
  ‘jss.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  18.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 181.9Mb
  sub-directories of 1Mb or more:
    extdata    5.4Mb
    libs     176.3Mb
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  23.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   9.0Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs     17.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.4Mb
'LazyData' is specified without a 'data' directory
installed size is 55.0Mb
  sub-directories of 1Mb or more:
    libs  54.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'GenomicRanges', 'org.Hs.eg.db', 'reactome.db', 'fgsea'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RMark.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 134.2Mb
  sub-directories of 1Mb or more:
    libs  133.8Mb
GNU make is a SystemRequirements.
installed size is 91.9Mb
  sub-directories of 1Mb or more:
    libs  91.1Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RmecabKo.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   7.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs       1.4Mb
    minizinc   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
'LazyData' is specified without a 'data' directory
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
GNU make is a SystemRequirements.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘recount3’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Missing or unexported object: 'SummarizedExperiment::colnames'
Error(s) in re-building vignettes:
  ...
--- re-building ‘data.Rmd’ using rmarkdown
--- finished re-building ‘data.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 88-89 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error:
! 'colnames' is not an exported object from 'namespace:SummarizedExperiment'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘pbdMPI’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package unavailable to check Rd xrefs: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 108.9Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     106.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  17.7Mb
Note: found 1 marked UTF-8 string
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’ ‘utils’
  All declared Imports should be used.
installed size is 70.1Mb
  sub-directories of 1Mb or more:
    libs  69.5Mb
GNU make is a SystemRequirements.
Note: found 6 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              4.8Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
'LazyData' is specified without a 'data' directory
sh: cmake: command not found
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
installed size is 55.1Mb
  sub-directories of 1Mb or more:
    libs  54.0Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    dependencies  24.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  28.0Mb
Note: found 467 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    help   1.4Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 187.4Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.8Mb
    libs  179.9Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
GNU make is a SystemRequirements.
installed size is 256.3Mb
  sub-directories of 1Mb or more:
    lib    26.5Mb
    libs  227.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Namespaces in Imports field not imported from:
  ‘bitops’ ‘httpuv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is 108.5Mb
  sub-directories of 1Mb or more:
    libs  108.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R           2.0Mb
    bootstrap   1.6Mb
    doc         1.2Mb
    help        2.8Mb
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmarkdown   6.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs       2.4Mb
    projects   2.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data      4.1Mb
    extdata   1.4Mb
    libs      3.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'showtext', 'sysfonts'
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
installed size is 58.2Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘lubridate’ ‘rstantools’
  All declared Imports should be used.
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.8Mb
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘rWikiPathways’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    libs  47.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 63.3Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     57.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RVowpalWabbit.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    extdata   2.4Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.2Mb
    yacas   1.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs    8.9Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 37 marked Latin-1 strings
  Note: found 172 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 63 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘Matrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
'LazyData' is specified without a 'data' directory
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  43.7Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.4Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'org.Sc.sgd.db'
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.4Mb
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following executable file:
  inst/extdata/Azores.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pcalg’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Packages suggested but not available for checking:
  'DropletUtils', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘Nebulosa’
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DuoClustering2018’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocSingular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Nebulosa', 'infercnv', 'UCell', 'AUCell'
Package unavailable to check Rd xrefs: ‘infercnv’
Unknown package ‘UCell’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘oligoClasses’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
Package unavailable to check Rd xrefs: ‘INLA’
Found the following executable file:
  inst/shape/GermanyNUTS3.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.0Mb
Note: found 3 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  15.4Mb
GNU make is a SystemRequirements.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.6Mb
Package suggested but not available for checking: ‘rsbml’
Package required but not available: ‘tximport’

Package suggested but not available for checking: ‘ArrayExpress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘datawizard’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.5Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs    20.4Mb
    models   1.6Mb
Note: found 836 marked UTF-8 strings
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.3Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.3Mb
Note: found 3128 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 52 marked UTF-8 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  11.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Packages suggested but not available for checking:
  'GenomicAlignments', 'GenomicRanges', 'muscle', 'Rsamtools'
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.3Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘monocle’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 283.1Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    libs    276.8Mb
    sqlite    1.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.9Mb
Found the following executable files:
  inst/extdata/access.dbf
  inst/extdata/existing.dbf
  inst/extdata/existingna.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    www   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> X \in \mathbb 
                         {R}{n\times p}
l.3262 ...data \eqn{X \in \mathbb{R}{n\times p}}{}
                                                   such that its rows are
! Undefined control sequence.
<argument> ...Delta _{p-1} =\lbrace z \in \mathbb 
                                                  {R}^p~|~z_j > 0, \sum _{i=...
l.3265 }{}
           test whether the data is uniformly distributed.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package suggested but not available for checking: ‘copynumber’
Package required and available but unsuitable version: ‘GenomeInfoDb’

Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
GNU make is a SystemRequirements.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  11.7Mb
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Package suggested but not available for checking: ‘clipper’
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  21.4Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   7.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.1Mb
GNU make is a SystemRequirements.
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘gurobi’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 1122 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.3Mb
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘snapKrig-Ex.R’ failed
The error most likely occurred in:

> ### Name: Math.sk
> ### Title: Math group generics
> ### Aliases: Math.sk
> 
> ### ** Examples
> 
> g = sk_validate(list(gval=stats::rnorm(4^2), gdim=4, gres=0.5))
> summary(g)
complete sk grid
16 points
range [-2.21, 1.60]
..............................
Error in sk_make(g) : argument gdim not found
Calls: summary ... summary.sk -> apply -> sk_coords -> sk -> sk_validate -> sk_make
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘snapKrig_introduction.Rmd’ using rmarkdown
Quitting from lines 60-67 (snapKrig_introduction.Rmd) 
Error: processing vignette 'snapKrig_introduction.Rmd' failed with diagnostics:
argument gdim not found
--- failed re-building ‘snapKrig_introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘snapKrig_introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      3.3Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘itertools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.1Mb
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘sos.Rnw’ using Sweave
Loading required package: brew

Attaching package: 'sos'

The following object is masked from 'package:utils':

    ?
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DropletUtils’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.0Mb
Package suggested but not available for checking: ‘r2cytoscape’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  13.5Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  37.1Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    java   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is 54.6Mb
  sub-directories of 1Mb or more:
    libs  53.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.5Mb
Note: found 283 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.9Mb
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
Note: found 34 marked UTF-8 strings
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Found the following executable files:
  inst/extdata/SouthernBuh-habitats_shapefile.dbf
  inst/extdata/test_shapefile.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Note: found 189 marked UTF-8 strings
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘psy’ ‘ranger’
  All declared Imports should be used.
Package suggested but not available for checking: ‘antaresViz’
Package unavailable to check Rd xrefs: ‘antaresViz’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
--- finished re-building ‘basics.Rmd’

--- re-building ‘guide.Rmd’ using rmarkdown
--- finished re-building ‘guide.Rmd’

--- re-building ‘technical.Rmd’ using rmarkdown
! kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10

! mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied

! mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.

! kpathsea: Appending font creation commands to missfont.log.

Error: processing vignette 'technical.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.1/spmodel.Rcheck/vign_test/spmodel/vignettes/technical.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See technical.log for more info.
--- failed re-building ‘technical.Rmd’

SUMMARY: processing the following file failed:
  ‘technical.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   2.6Mb
    libs     12.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
Note: found 7587 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is 59.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  57.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs  10.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  26.1Mb
'LazyData' is specified without a 'data' directory
installed size is 97.9Mb
  sub-directories of 1Mb or more:
    libs  97.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Note: found 40748 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 302-324 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
duplicated values in No.pas
--- failed re-building ‘stacomir.Rmd’

SUMMARY: processing the following file failed:
  ‘stacomir.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
installed size is 52.8Mb
  sub-directories of 1Mb or more:
    libs  52.4Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       2.0Mb
installed size is 85.8Mb
  sub-directories of 1Mb or more:
    libs  85.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    1.7Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 18 marked UTF-8 strings
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.4Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Package required but not available: ‘pvca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
Package suggested but not available for checking: ‘INLA’
installed size is 65.3Mb
  sub-directories of 1Mb or more:
    libs  64.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Data codoc mismatches from documentation object 'SLCS':
Variables in data frame 'SLCS'
  Code: SLCS_1 SLCS_10 SLCS_11 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
  Docs: SLCS_11 SLCS_1 SLCS_10 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.7Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘Rsymphony’
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Note: found 83 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.3Mb
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...! \perp T_1 | \tilde {S}_1 \; \text 
                                                  {and} \; \tilde {S}_1 \per...
l.3471 ...perp \!\!\! \perp T_0 | \tilde{S}_0 .}{}
                                                   This can informally be
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocParallel’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sf', 'INLA'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    2.2Mb
    libs   1.6Mb
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
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Running examples in ‘survival-Ex.R’ failed
The error most likely occurred in:

> ### Name: concordance
> ### Title: Compute the concordance statistic for data or a model
> ### Aliases: concordance concordance.coxph concordance.formula
> ###   concordance.lm concordance.survreg
> ### Keywords: survival
> 
> ### ** Examples
> 
> fit1 <- coxph(Surv(ptime, pstat) ~ age + sex + mspike, mgus2)
> concordance(fit1, timewt="n/G2")  # Uno's weighting
Call:
concordance.coxph(object = fit1, timewt = "n/G2")

n= 1373 
Concordance= 0.6132 se= 0.1026
concordant discordant     tied.x     tied.y    tied.xy 
 461425.07  290956.09     265.66     120.39       0.00 
> 
> # logistic regression 
> fit2 <- glm(I(sex=='M') ~ age + log(creatinine), binomial, data= flchain)
> concordance(fit2)  # equal to the AUC
Error in (function (y, x, strata, weights, ymin = NULL, ymax = NULL, timewt = c("n",  : 
  left hand side of the formula must be a numeric vector,
 survival object, or an orderable factor
Calls: concordance ... eval -> eval -> <Anonymous> -> eval -> eval -> <Anonymous>
Execution halted
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Package unavailable to check Rd xrefs: ‘survJamda’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is 50.3Mb
  sub-directories of 1Mb or more:
    libs  49.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘udunits2’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    fonts   1.7Mb
    libs   15.5Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 81 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 301 marked UTF-8 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘biblio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dearseq’
Package unavailable to check Rd xrefs: ‘dearseq’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    apps   2.3Mb
    libs  10.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  18.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      2.4Mb
    telemac   1.0Mb
Package suggested but not available for checking: ‘INLA’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 314.0Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs  310.7Mb
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.6Mb
    tessdata  22.2Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.0Mb
    libs   4.1Mb
Missing or unexported object: ‘Matrix::rowScale’
Running examples in ‘text2vec-Ex.R’ failed
The error most likely occurred in:

> ### Name: BNS
> ### Title: BNS
> ### Aliases: BNS
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("movie_review")
> N = 1000
> it = itoken(head(movie_review$review, N), preprocessor = tolower, tokenizer = word_tokenizer)
> vocab = create_vocabulary(it)
> dtm = create_dtm(it, vocab_vectorizer(vocab))
as(<dgTMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead
> model_bns = BNS$new()
> dtm_bns = model_bns$fit_transform(dtm, head(movie_review$sentiment, N))
Error: 'colScale' is not an exported object from 'namespace:Matrix'
Execution halted
Running ‘testthat.R’ [21s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   7. │     └─text2vec::normalize(x_internal, private$norm)
   8. └─base::.handleSimpleError(...)
   9.   └─base (local) h(simpleError(msg, call))
  ── Error ('test-s3-interface.R:41:3'): S3 bns ──────────────────────────────────
  Error: 'colScale' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─mlapi::fit_transform(dtm, bns, y) at test-s3-interface.R:41:2
   2. └─mlapi:::fit_transform.Matrix(dtm, bns, y)
   3.   └─model$fit_transform(x, y = y, ...)
   4.     └─self$transform(x, ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 80 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘files-multicore.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'files-multicore.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘files-multicore.Rmd’

--- re-building ‘glove.Rmd’ using rmarkdown
--- finished re-building ‘glove.Rmd’

--- re-building ‘text-vectorization.Rmd’ using rmarkdown
Quitting from lines 280-281 (text-vectorization.Rmd) 
Error: processing vignette 'text-vectorization.Rmd' failed with diagnostics:
'rowScale' is not an exported object from 'namespace:Matrix'
--- failed re-building ‘text-vectorization.Rmd’

SUMMARY: processing the following file failed:
  ‘text-vectorization.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.8Mb
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_{i} - \text 
                         {min}(\mathbf {x})
l.447 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> \text 
                 {max}(\mathbf {x}) - \text {min}(\mathbf {x})
l.447 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> \text {max}(\mathbf {x}) - \text 
                                            {min}(\mathbf {x})
l.447 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> x_{i} - \text 
                         {median}(\mathbf {x})
l.654 ...\mathbf{x})/{1.35}}\right)\right]^{-1}}{}
                                                  
! Undefined control sequence.
<argument> \text 
                 {IQR}(\mathbf {x})/{1.35}
l.654 ...\mathbf{x})/{1.35}}\right)\right]^{-1}}{}
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sysfonts', 'showtext'
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    data   3.1Mb
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  56.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’ ‘tidybins’ ‘validata’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
Note: found 4546 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  60.3Mb
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   4.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs    13.1Mb
    tiledb  26.7Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2750 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.965 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.965 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.965 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1021 visjs documentation}}
                            .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1021 visjs documentation}}
                            .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1021 visjs documentation}}
                            .
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  44.7Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.4Mb
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    examples  12.0Mb
    include    3.6Mb
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
installed size is 199.9Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       1.6Mb
    include    1.5Mb
    libs     190.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Quitting from lines 86-87 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix
Loading required package: fds
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl

Attaching package: 'fda'

The following object is masked from 'package:graphics':

    matplot

--- finished re-building 'trackeR.Rnw'

SUMMARY: processing the following file failed:
  ‘TourDetrackeR.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
'LazyData' is specified without a 'data' directory
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  49.1Mb
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   2.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.3Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 121.2Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  116.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.0Mb
    libs  66.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       21.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   4.3Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
'LazyData' is specified without a 'data' directory
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls not declared from:
  ‘unitizerdummypkg1’ ‘unitizerdummypkg2’
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 47.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  43.5Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 7872 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
Note: found 1 marked UTF-8 string
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 33 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  23.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking:
  'vaersNDvax', 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 270.4Mb
  sub-directories of 1Mb or more:
    extdata    2.7Mb
    libs     266.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘taxlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    help   3.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  53.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.0Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  60.6Mb
Note: found 4954 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 85.8Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   5.5Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1668 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocParallel’
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.4Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘vdiffr’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   7.9Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    bin   4.2Mb
    lib   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 57.0Mb
  sub-directories of 1Mb or more:
    libs  56.1Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    java  27.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is 50.9Mb
  sub-directories of 1Mb or more:
    libs  50.6Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 48.8Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Package suggested but not available for checking: ‘SDMTools’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 86.4Mb
  sub-directories of 1Mb or more:
    libs  85.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Package required but not available: ‘BSgenome.Mmusculus.UCSC.mm10’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.0Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Package suggested but not available for checking: ‘HiTC’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       2.0Mb
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Running ‘tinytest.R’ [14s/15s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    
  test_crs.R....................    0 tests    Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'rast': could not find function "CRS"
  Calls: <Anonymous> ... raster -> raster -> .local -> .handleSimpleError -> h
  In addition: Warning message:
  In steps.track_xyt(t2) : burst's are ignored, use steps_by_burst instead.
  Execution halted
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 231 marked UTF-8 strings
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.1Mb
    testdata   2.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 88.6Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs  83.8Mb
Note: found 1409 marked UTF-8 strings
Package which this enhances but not available for checking: ‘ARTP’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘autocart-intro.Rmd’ using rmarkdown
Loading required package: fields
Loading required package: spam
Spam version 2.8-0 (2022-01-05) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite

Try help(fields) to get started.
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘AzureKeyVault’
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘baffle.Rmd’ using rmarkdown
Quitting from lines 88-95 (baffle.Rmd) 
Error: processing vignette 'baffle.Rmd' failed with diagnostics:
unused arguments (title.font = 2, title.cex = 1.5)
--- failed re-building ‘baffle.Rmd’

SUMMARY: processing the following file failed:
  ‘baffle.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  75.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is 67.6Mb
  sub-directories of 1Mb or more:
    libs  66.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/banditpam.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/bapred.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Note: found 13825 marked UTF-8 strings
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.3Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GO.db', 'org.Hs.eg.db', 'reactome.db'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
installed size is 62.8Mb
  sub-directories of 1Mb or more:
    libs  60.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 83.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  82.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   5.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.2Mb
installed size is 69.4Mb
  sub-directories of 1Mb or more:
    libs  68.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 83.6Mb
  sub-directories of 1Mb or more:
    libs  82.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
GNU make is a SystemRequirements.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  14.3Mb
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  20.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.9Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  15.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
GNU make is a SystemRequirements.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.5Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BRugs’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 79.0Mb
  sub-directories of 1Mb or more:
    libs  77.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  43.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
'LazyData' is specified without a 'data' directory
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  56.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Note: found 10089 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    help   1.1Mb
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   6.2Mb
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 151.5Mb
  sub-directories of 1Mb or more:
    include  151.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/biblio.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.3Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.9Mb
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help   1.5Mb
    libs   4.7Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.2Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is 75.3Mb
  sub-directories of 1Mb or more:
    libs  74.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘desc’ ‘lme4’ ‘mitml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      2.8Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Note: found 46 marked UTF-8 strings
Package suggested but not available for checking: ‘rpanel’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Package suggested but not available for checking: ‘IHW’
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    libs  38.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘digest’ ‘ergm’ ‘foreign’ ‘gWidgets2’ ‘gWidgets2tcltk’ ‘haven’
  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 75.8Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs      73.2Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.8Mb
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
installed size is 123.0Mb
  sub-directories of 1Mb or more:
    libs  122.2Mb
GNU make is a SystemRequirements.
installed size is 78.3Mb
  sub-directories of 1Mb or more:
    libs  77.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 76.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  69.2Mb
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Package suggested but not available for checking: ‘sangerseqR’
installed size is 394.5Mb
  sub-directories of 1Mb or more:
    include   10.2Mb
    lib      384.0Mb
GNU make is a SystemRequirements.
installed size is 78.3Mb
  sub-directories of 1Mb or more:
    libs  77.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is 80.6Mb
  sub-directories of 1Mb or more:
    libs  80.4Mb
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.5Mb
Package suggested but not available for checking: ‘glmmADMB’
Found the following significant warnings:
  Warning: multiple methods tables found for ‘export’
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Brundle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    help   1.3Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    fonts   3.0Mb
    lib     4.9Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs  27.6Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 103.9Mb
  sub-directories of 1Mb or more:
    libs  103.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 49.6Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is 61.9Mb
  sub-directories of 1Mb or more:
    libs  61.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Note: found 287 marked UTF-8 strings
Note: found 512 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Note: found 1 marked UTF-8 string
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    libs  38.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
>   
> data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+ norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
+ mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
sh: mageck: command not found
Warning in system(mageckstring) : error in running command
Warning in file(file, "rt") :
  cannot open file 'TEST.gene_summary.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: stat.mageck -> load.file -> read.table -> file
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
sh: mageck: command not found
Quitting from lines 1956-1959 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CaRpools.Rmd’

SUMMARY: processing the following file failed:
  ‘CaRpools.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  27.3Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.4Mb
'LazyData' is specified without a 'data' directory
installed size is 133.7Mb
  sub-directories of 1Mb or more:
    libs  133.3Mb
GNU make is a SystemRequirements.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CirceR’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
Note: found 907 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.2Mb
    libs  10.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/cequre.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
installed size is 120.7Mb
  sub-directories of 1Mb or more:
    libs  120.5Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GenomicInteractions', 'countreg'
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Package required but not available: ‘TxDb.Mmusculus.UCSC.mm10.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28982 marked UTF-8 strings
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_clipp.Rmd’ using rmarkdown
Error: processing vignette 'using_clipp.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘using_clipp.Rmd’

SUMMARY: processing the following file failed:
  ‘using_clipp.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kernlab’
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...{C}=c\mathbf {U}\cdot \operatorname 
                                                  {diag}(\mathbf {s}) + \mat...
l.147 \mathbf{1}\,\mathbf{o}^T}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'GO.db', 'moe430a.db'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/cold.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CAM’
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.9Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
installed size is 59.9Mb
  sub-directories of 1Mb or more:
    libs  58.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.6Mb
    libs   3.2Mb
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs          2.8Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.6Mb
Note: found 139613 marked UTF-8 strings
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
Note: found 1934235 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Running ‘testthat.R’ [60s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-labels.R:200:3'): clean_names_with_labels ────────────────────
  names(cleaned) (`actual`) not equal to c("name_with_space", "TwoWords", "total_2009", "accents") (`expected`).
  
  `actual`:   "name_with_space" "TwoWords" "total_2009" "`acc'ents"
  `expected`: "name_with_space" "TwoWords" "total_2009" "accents"  
  ── Failure ('test-labels.R:201:3'): clean_names_with_labels ────────────────────
  get_label(cleaned) (`actual`) not equal to c(...) (`expected`).
  
  `names(actual)`:   "name_with_space" "TwoWords" "total_2009" "`acc'ents"
  `names(expected)`: "name_with_space" "TwoWords" "total_2009" "accents"  
  
  [ FAIL 2 | WARN 0 | SKIP 45 | PASS 334 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v79’
Running ‘testthat.R’ [28s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `loadNamespace(x)`: there is no package called 'EnsDb.Hsapiens.v79'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(length(as_gene_symbol(entrez_test)), length(entrez_test)) at test-utils.R:16:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─crosstalkr::as_gene_symbol(entrez_test)
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base (local) withOneRestart(expr, restarts[[1L]])
   8.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 2 | SKIP 8 | PASS 89 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 500 marked UTF-8 strings
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Notation.Rmd’ using rmarkdown
Error: processing vignette 'Notation.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Notation.Rmd’

--- re-building ‘Terminology.Rmd’ using rmarkdown
Error: processing vignette 'Terminology.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Terminology.Rmd’

--- re-building ‘Using-assess.Rmd’ using rmarkdown
Error: processing vignette 'Using-assess.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Using-assess.Rmd’

--- re-building ‘cSEM.Rmd’ using rmarkdown
Error: processing vignette 'cSEM.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘cSEM.Rmd’

SUMMARY: processing the following files failed:
  ‘Notation.Rmd’ ‘Terminology.Rmd’ ‘Using-assess.Rmd’ ‘cSEM.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Note: found 3031 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 1350 marked UTF-8 strings
installed size is 138.9Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    data    1.5Mb
    libs  135.0Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    deps  10.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
Note: found 36560 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
installed size is 58.8Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs    1.2Mb
    tests   1.5Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
Running ‘tinytest.R’ [1s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test.R........................  131 tests [0;31m2 fails[0m 
  test.R........................  131 tests [0;31m2 fails[0m 
  test.R........................  132 tests [0;31m2 fails[0m 
  test.R........................  133 tests [0;31m2 fails[0m 
  test.R........................  134 tests [0;31m2 fails[0m [0;34m0.4s[0m
  ----- FAILED[data]: test.R<35--36>
   call| expect_equal(convert_date(41824.625, "excel", fraction = TRUE), 
   call| -->    structure(1404478800, class = c("POSIXct", "POSIXt"), tzone = ""))
   diff| Expected '2014-07-04 09:00:00', got '2014-07-04 15:00:00'
  ----- FAILED[data]: test.R<37--38>
   call| expect_equal(convert_date(610.125, "excel", fraction = TRUE), 
   call| -->    structure(-2156450400, class = c("POSIXct", "POSIXt"), tzone = ""))
   diff| Expected '1901-08-31 21:00:00', got '1901-09-01 03:00:00'
  Error: 2 out of 134 tests failed
  Execution halted
'LazyData' is specified without a 'data' directory
Note: found 54315 marked UTF-8 strings
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.7Mb
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘bslib’ ‘knitr’ ‘matrixStats’ ‘rmarkdown’ ‘shinythemes’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-portable flags in variable 'PKG_FFLAGS':
  -std=f2008
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘plyr’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  56.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  13.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 8014 marked UTF-8 strings
Package suggested but not available for checking: ‘rlibkriging’
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'library' or 'require' calls not declared from:
  ‘MASS’ ‘Matrix’ ‘NNMF’ ‘RANN’ ‘RSpectra’ ‘c’ ‘coRanking’ ‘ggplot’
  ‘igraph’ ‘loe’ ‘scales’ ‘tidyr’
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  56.9Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘truncnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.2Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  11.6Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rjson’ ‘uuid’
  All declared Imports should be used.
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Running ‘simpleTests.R’ [0s/0s]
  Running ‘skeleton_git2r.R’ [3s/3s]
Running the tests in ‘tests/skeleton_git2r.R’ failed.
Last 13 lines of output:
  * saving partial Rd database
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘foo_1.0.tar.gz’
  
  dratting
  Added and committed foo_1.0.tar.gz plus PACKAGES files. Still need to push.
  
  Error in testRepoActions(repodir) : 
    Wrong package files found after pruning for version = NA
  Calls: runTest -> testRepoActions
  In addition: Warning message:
  In (function (dir = ".", fields = NULL, type = c("source", "mac.binary",  :
    PACKAGES files do not include MD5 sums in the win.binary case, so strict checking is impossible. Calling down to write_PACKAGES directly.
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    tutorials   5.2Mb
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
installed size is 69.0Mb
  sub-directories of 1Mb or more:
    libs  68.6Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> f:\mathbb 
                     {R}^K \to \mathbb {R}^L, (x_{n1},x_{n2},...,x_{nK}) \ma...
l.2280 ...) \mapsto f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
! Undefined control sequence.
<argument> f:\mathbb {R}^K \to \mathbb 
                                       {R}^L, (x_{n1},x_{n2},...,x_{nK}) \ma...
l.2280 ...) \mapsto f(x_{n1},x_{n2},...,x_{nK})}{}
                                                   be differentiable up to o...
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Package suggested but not available for checking: ‘dsBaseClient’
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.6Mb
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.8Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 284.6Mb
  sub-directories of 1Mb or more:
    libs  284.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  24.1Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   7.3Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Codoc mismatches from documentation object 'IQLearnFS_VHet-methods':
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
Note: found 9 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   7.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs        8.5Mb
    shiny_app   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  11.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘org.Hs.eg.db’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’ ‘urca’
  All declared Imports should be used.
installed size is 91.6Mb
  sub-directories of 1Mb or more:
    libs  90.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘econet.tex’ using tex
Error: processing vignette 'econet.tex' failed with diagnostics:
Running 'texi2dvi' on 'econet.tex' failed.
LaTeX errors:
! LaTeX Error: File `orcidlink.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \graphicspath
                 {{Figures/}}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘econet.tex’

SUMMARY: processing the following file failed:
  ‘econet.tex’

Error: Vignette re-building failed.
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 77.4Mb
  sub-directories of 1Mb or more:
    libs  76.8Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown
! Missing endcsname inserted.
<to be read again> 
                   unhbox 
l.301 ...ics[width=1\linewidth]{./images/Figure_1}

Error: processing vignette 'Introduction_to_eHDPrep.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/high-sierra-x86_64/results/4.1/eHDPrep.Rcheck/vign_test/eHDPrep/vignettes/Introduction_to_eHDPrep.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Introduction_to_eHDPrep.log for more info.
--- failed re-building ‘Introduction_to_eHDPrep.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_eHDPrep.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
installed size is 130.2Mb
  sub-directories of 1Mb or more:
    libs  130.0Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 58.1Mb
  sub-directories of 1Mb or more:
    libs  56.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 50 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  15.3Mb
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Note: found 16919 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.7Mb
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘rgdal’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMMAgeo’ ‘limSolve’ ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘EstimationTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: legend.HazardShape
> ### Title: Customize legend for 'plot.HazardShape' outputs
> ### Aliases: legend.HazardShape
> 
> ### ** Examples
> 
> library(EstimationTools)
> 
> data("reduction_cells")
> TTT_IG <- TTTE_Analytical(Surv(days, status) ~ 1, data = reduction_cells,
+                           method = 'censored')
> HS_IG <- TTT_hazard_shape(TTT_IG, data = reduction_cells)
> 
> #----------------------------------------------------------------------------
> # Example 1: put legend to the TTT plot of the reduction cells data set.
> 
> # Run `plot.HazardShape` method.
> par(
+   cex.lab=1.8,
+   cex.axis=1.8,
+   mar=c(4.8,5.4,1,1),
+   las = 1,
+   mgp=c(3.4,1,0)
+ )
> plot(HS_IG, pch = 16, cex = 1.8)
> 
> # Finally, put the legend
> legend.HazardShape(
+   x = "bottomright",
+   box.lwd = NA,
+   cex = 1.8,
+   pt.cex = 1.8,
+   bty = 'n',
+   pch = c(16, NA)
+ )
Error in legend(x, y, legend, fill, col, border, lty, lwd, pch, angle,  : 
  unused arguments (title.font, seg.len)
Calls: legend.HazardShape
Execution halted
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Packages required and available but unsuitable versions: 'grid', 'splines'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Running ‘testthat.R’ [28s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_helper_blocksize.R:34:3'): blockSize reports block size in row-col order ──
  Error: [writeRaster] invalid driver
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_helper_blocksize.R:34:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─terra::writeRaster(...) at test_helper_blocksize.R:35:4
   4. └─terra::writeRaster(...)
   5.   └─terra (local) .local(x, filename, ...)
   6.     └─terra:::messages(x, "writeRaster")
   7.       └─terra:::error(f, x@ptr$getError())
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 463 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    exiftool  14.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
installed size is 76.5Mb
  sub-directories of 1Mb or more:
    libs  74.3Mb
GNU make is a SystemRequirements.
Package required and available but unsuitable version: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/fastAFT.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   1.2Mb
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.9Mb
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    libs  47.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
Package suggested but not available for checking: ‘coxKM’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
Package suggested but not available for checking: ‘NNLM’
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.9Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fastverse_intro.Rmd’ using rmarkdown
Quitting from lines 104-108 (fastverse_intro.Rmd) 
Error: processing vignette 'fastverse_intro.Rmd' failed with diagnostics:
package or namespace load failed for 'fastverse':
 .onAttach failed in attachNamespace() for 'fastverse', details:
  call: NULL
  error: package or namespace load failed for 'magrittr':
 .onLoad failed in loadNamespace() for 'magrittr', details:
  call: fun(libname, pkgname)
  error: object 'magrittr_init' not found
--- failed re-building ‘fastverse_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘fastverse_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   6.7Mb
Unexported objects imported by ':::' calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Note: found 75 marked UTF-8 strings
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
Note: found 76 marked UTF-8 strings
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs  36.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       1.9Mb
    extdata   2.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    lib   11.1Mb
    libs  19.7Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Running ‘testthat.R’ [27s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(fitHeavyTail)
  > 
  > test_check("fitHeavyTail")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fit_mvst.R:43:3'): default mode works ────────────────────────
  ...[] not equal to ...[].
  Component "num_iterations": Mean relative difference: 0.002739726
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 82 marked UTF-8 strings
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 256.2Mb
  sub-directories of 1Mb or more:
    libs  255.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/FLSSS.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘Rcpp’ ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.6Mb
    libs   7.5Mb
Note: found 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   5.5Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 81.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.7Mb
    libs  74.2Mb
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘foba’
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘WGCNA’
'LazyData' is specified without a 'data' directory
File ‘fuzzyRankTests/libs/fuzzyRankTests.so’:
  Found non-API calls to R: ‘signrank_free’, ‘wilcox_free’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cBioPortalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Note: found 2 marked UTF-8 strings
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.6Mb
installed size is 68.6Mb
  sub-directories of 1Mb or more:
    libs  68.1Mb
GNU make is a SystemRequirements.
installed size is 60.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     56.8Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: ‘gputools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

SUMMARY: processing the following file failed:
  ‘gcbd.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 294.1Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    290.8Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.4Mb
    libs      1.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘muscle’
Package suggested but not available for checking: ‘rrvgo’
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.9Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   3.0Mb
    libs      4.4Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyr’
  All declared Imports should be used.
Note: found 80 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 646 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.2Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 50.6Mb
  sub-directories of 1Mb or more:
    libs  49.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘GWmodel’ ‘beepr’ ‘cartography’ ‘dplyr’ ‘raster’ ‘readxl’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinyjs’ ‘sp’
  ‘spdep’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions:
  'biomaRt', 'grDevices', 'graphics', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...s ,C_k)^\top = \mathbf {0}\,\,\text 
                                                  {and}\,\,\mathcal H_0: \ma...
l.236 ...H} (B_1,\ldots,B_k)^\top = \mathbf{0},}{}
                                                  
! Undefined control sequence.
<argument> ...\mathbf {C} = \mathbf {0}\,\, \text 
                                                  {or}\,\,\mathcal H_{0,\ell...
l.247 ...{B} = \mathbf{0}, \,\,\ell=1,\ldots,q,}{}
                                                  
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.249 ...s \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.250 \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                             , respectively, are calculated.
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.263 ...r \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.264 for \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                                 , the test statistics and c...
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Package required but not available: ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘do’ ‘survival’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  18.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Packages required but not available: 'memes', 'universalmotif'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggOceanMapsData’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lefser', 'Maaslin2', 'metagenomeSeq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    doc   1.9Mb
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
Note: found 203 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘refund’ ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19.masked’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 149.5Mb
  sub-directories of 1Mb or more:
    doc     1.4Mb
    libs  147.2Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    libs  49.4Mb
GNU make is a SystemRequirements.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘GMMBoost’
  All declared Imports should be used.
installed size is 53.2Mb
  sub-directories of 1Mb or more:
    libs  52.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 67.4Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs           62.2Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.4Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.2Mb
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
installed size is 140.6Mb
  sub-directories of 1Mb or more:
    libs  139.7Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cubature’ ‘magicaxis’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Note: found 989 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Running ‘testpage.R’ [1s/1s]
Running the tests in ‘tests/testpage.R’ failed.
Last 13 lines of output:
  > # Now import testpage.ps and draw it in various ways
  > #######################################
  > 
  > require(grImport)
  Loading required package: grImport
  Loading required package: XML
  > 
  > PostScriptTrace("testpage.ps", "testpage.xml")
  sh: gs: command not found
  Error in PostScriptTrace("testpage.ps", "testpage.xml") : 
    sorry, 'gs' cannot be found
  In addition: Warning message:
  In system(paste(shQuote(gsexe), "-help > /dev/null")) :
    error in running command
  Execution halted
Errors in running code in vignettes:
when running code in ‘import.Rnw’
  ...
Loading required package: XML

> PostScriptTrace("chess_game_01.fromInkscape.eps")
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

  When sourcing 'import.R':
Error: sorry, 'gs' cannot be found
Execution halted
when running code in ‘importText.Rnw’
  ...
Loading required package: XML

> PostScriptTrace("hello.ps", "hello.xml")
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

  When sourcing 'importText.R':
Error: sorry, 'gs' cannot be found
Execution halted

  ‘import.Rnw’... failed
  ‘importText.Rnw’... failed
Error(s) in re-building vignettes:
--- re-building ‘import.Rnw’ using Sweave
Loading required package: XML
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

Error: processing vignette 'import.Rnw' failed with diagnostics:
 chunk 5 (label = chesspiece) 
Error in PostScriptTrace("chess_game_01.fromInkscape.eps") : 
  sorry, 'gs' cannot be found

--- failed re-building 'import.Rnw'

--- re-building ‘importText.Rnw’ using Sweave
Loading required package: XML
sh: gs: command not found
Warning in system(paste(shQuote(gsexe), "-help > /dev/null")) :
  error in running command

Error: processing vignette 'importText.Rnw' failed with diagnostics:
 chunk 4 (label = simpleimport) 
Error in PostScriptTrace("hello.ps", "hello.xml") : 
  sorry, 'gs' cannot be found

--- failed re-building 'importText.Rnw'

SUMMARY: processing the following files failed:
  ‘import.Rnw’ ‘importText.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
Package required but not available: ‘CelliD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.8Mb
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Note: found 18981 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.7Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 182.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  179.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs    1.6Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Found the following executable file:
  inst/extdata/penmarch.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 110.3Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  108.5Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘questionr’ ‘rprojroot’ ‘tidyverse’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Heatplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
GNU make is a SystemRequirements.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  19.3Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fmrs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
':::' call which should be '::': ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.6Mb
Package required and available but unsuitable version: ‘fitHeavyTail’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.9Mb
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    libs  42.1Mb
GNU make is a SystemRequirements.
Note: found 9638 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 64.7Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Package required but not available: ‘bamsignals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    libs  58.6Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘HTSFilter’
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘webshot2’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.7Mb
Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
Note: found 55 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  31.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ie2miscdata’
Note: found 1 marked UTF-8 string
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.4Mb
    libs  14.6Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         4.5Mb
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     23.0Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Package required but not available: ‘RankProd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: ‘optimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Error(s) in re-building vignettes:
  ...
--- re-building ‘calculations.Rmd’ using rmarkdown
Error: processing vignette 'calculations.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘calculations.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘intro.Rmd’

--- re-building ‘plots.Rmd’ using rmarkdown
Error: processing vignette 'plots.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘plots.Rmd’

SUMMARY: processing the following files failed:
  ‘calculations.Rmd’ ‘intro.Rmd’ ‘plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘methods’ ‘mlbench’ ‘parallel’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  32.0Mb
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
Note: found 12106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘surveyspec’
Note: found 102 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Package suggested but not available for checking: ‘Rmpi’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7528 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘modules’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    libs  52.0Mb
GNU make is a SystemRequirements.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  13.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Running examples in ‘ispdata-Ex.R’ failed
The error most likely occurred in:

> ### Name: bicycle_theft
> ### Title: Access the statistics about bicycle theft of the State of Rio de
> ###   Janeiro
> ### Aliases: bicycle_theft
> 
> ### ** Examples
> 
> bicycle_theft()
ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.
Error in open.connection(3L, "rb") : 
  Timeout was reached: [www.ispdados.rj.gov.br] Connection timed out after 10112 milliseconds
Calls: bicycle_theft ... <Anonymous> -> vroom_ -> <Anonymous> -> open.connection
Execution halted
Running ‘testthat.R’ [2s/313s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   5.     ├─openxlsx::read.xlsx(...)
   6.     └─openxlsx:::read.xlsx.default(...)
   7.       └─openxlsx:::getFile(xlsxFile)
   8.         └─utils::download.file(...)
  
  [ FAIL 11 | WARN 4 | SKIP 0 | PASS 0 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (i in seq_len(n)) { :
    closing unused connection 9 (https://www.ispdados.rj.gov.br/Arquivos/UppEvolucaoMensalDeTitulos.csv)
  2: In for (i in seq_len(n)) { :
    closing unused connection 8 (https://www.ispdados.rj.gov.br/Arquivos/PopulacaoEvolucaoMensalCisp.csv)
  3: In for (i in seq_len(n)) { :
    closing unused connection 7 (https://www.ispdados.rj.gov.br/Arquivos/BaseDPEvolucaoMensalCisp.csv)
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.6Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    docs   3.5Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 461377 marked UTF-8 strings
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  41.4Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘knitr’ ‘markdown’
  All declared Imports should be used.
Note: found 85 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’
  ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.9Mb
Package which this enhances but not available for checking: ‘MRCE’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘boot’ ‘fds’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Note: found 176 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘keras’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Hs.eg.db’
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc              1.1Mb
    libs             5.7Mb
    shiny-landsepi   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/LCMSQA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Note: found 1096 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  56.4Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘glue’ ‘stringr’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘airway’
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.4Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    libs  66.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      8.8Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.6Mb
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 435 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Note: found 266 marked UTF-8 strings
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      22.4Mb
    testdata   1.3Mb
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  56.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘agridat’ ‘ggplot2’ ‘maps’ ‘sp’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘base’ ‘qpdf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

SUMMARY: processing the following file failed:
  ‘localsolver.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 994 marked Latin-1 strings
Package suggested but not available for checking: ‘RDRToolbox’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GeneticsPed’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Note: found 55 marked UTF-8 strings
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
'LazyData' is specified without a 'data' directory
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  48.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 71.0Mb
  sub-directories of 1Mb or more:
    libs  70.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘orthogene’
Unknown package ‘orthogene’ in Rd xrefs
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Note: found 134 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘maptools’ ‘sp’
  All declared Imports should be used.
installed size is 133.8Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    libs  126.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Package suggested but not available for checking: ‘dittoSeq’
Package suggested but not available for checking: ‘ssize’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   5.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17524 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Note: found 55 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         11.4Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Note: found 29618 marked UTF-8 strings
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 55 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
Note: found 1763 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Note: found 5210 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘wiggleplotr’
Package suggested but not available for checking: ‘flashier’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘gurobi’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
Package required but not available: ‘rolog’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   9.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
Running ‘Class+Meth.R’ [1s/1s]
Running the tests in ‘tests/Class+Meth.R’ failed.
Last 13 lines of output:
  >                                         # further  checkMatrix(), etc
  > if(interactive()) options(error = recover)
  > options(warn=1)# show as they happen
  > cat("doExtras:",doExtras,"\n")
  doExtras: FALSE 
  > 
  > no.Mcl <- function(cl) ## TRUE if MatrixClass() returns empty, i.e., have "no Matrix-pkg class"
  +     identical(Matrix:::MatrixClass(cl), character(0))
  > 
  > setClass("myDGC", contains = "dgCMatrix")
  > M <- new("myDGC", as(Matrix(c(-2:4, rep(0,9)), 4), "CsparseMatrix"))
  Error in if (...length() && any(...names() == "Dimnames")) .Object@Dimnames <- fixupDN(.Object@Dimnames) : 
    missing value where TRUE/FALSE needed
  Calls: new -> initialize -> initialize
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 18 marked UTF-8 strings
Note: found 54 marked UTF-8 strings
Note: found 66 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked Latin-1 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  10.7Mb
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 46 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘grDevices’ ‘httr’
  ‘knitr’ ‘openssl’ ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’
  ‘spelling’ ‘testthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.0Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
'LazyData' is specified without a 'data' directory
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 111.1Mb
  sub-directories of 1Mb or more:
    libs  109.9Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is 94.8Mb
  sub-directories of 1Mb or more:
    libs  94.7Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 89.3Mb
  sub-directories of 1Mb or more:
    libs  88.6Mb
GNU make is a SystemRequirements.
Note: found 37 marked UTF-8 strings
Package suggested but not available for checking: ‘genuMet’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Package required but not available: ‘metagenomeSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 58.4Mb
  sub-directories of 1Mb or more:
    libs  58.0Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   3.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.6Mb
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘webshot2’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.266 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   (\eqn{p > 1}{}) distribut...
! Undefined control sequence.
<recently read> \mathbb 
                        
l.268 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   distributed according to ...
'LazyData' is specified without a 'data' directory
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  19.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘qlcMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Note: found 9345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dada2', 'DECIPHER'
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘config’ ‘desc’ ‘dplyr’ ‘glue’ ‘withr’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    lib    9.2Mb
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘curl’ ‘jsonlite’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 83.3Mb
  sub-directories of 1Mb or more:
    libs  83.2Mb
installed size is 101.3Mb
  sub-directories of 1Mb or more:
    libs  100.7Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘GlobalAncova’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘karyoploteR’
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/mixhvg.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘a-mixKernelInstallation.Rmd’ using knitr
--- finished re-building ‘a-mixKernelInstallation.Rmd’

--- re-building ‘mixKernelUsersGuide.Rmd’ using knitr
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2

Loaded mixOmics 6.15.0
Thank you for using mixOmics!
Tutorials: http://mixomics.org
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at http://mixomics.org/contact-us
Cite us:  citation('mixOmics')

Loading required package: reticulate

Any bug reports or comments? Notify us at jerome.mariette@inrae.fr or https://forgemia.inra.fr/jerome.mariette/mixKernel/-/issues
Quitting from lines 147-162 (mixKernelUsersGuide.Rmd) 
Error: processing vignette 'mixKernelUsersGuide.Rmd' failed with diagnostics:
non-numeric argument to mathematical function
--- failed re-building ‘mixKernelUsersGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘mixKernelUsersGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 219.7Mb
  sub-directories of 1Mb or more:
    libs  219.3Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs  61.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Package which this enhances but not available for checking: ‘MoBPSmaps’
Packages required but not available: 'RaggedExperiment', 'ggbio'

Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   4.6Mb
Note: found 16 marked UTF-8 strings
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 13 marked UTF-8 strings
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs     3.1Mb
    raster   2.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.6Mb
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
installed size is 65.3Mb
  sub-directories of 1Mb or more:
    libs  64.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.5Mb
    libs   3.6Mb
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.9Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  17.4Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'switchBox', 'leukemiasEset'
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plsgenomics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
installed size is 81.6Mb
  sub-directories of 1Mb or more:
    libs  81.4Mb
installed size is 110.1Mb
  sub-directories of 1Mb or more:
    doc     4.0Mb
    libs  104.7Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘fields’ ‘optmatch’ ‘rcbalance’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::expect_null(...) at test-unstash.R:2:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─mustashe::stash(...)
   5.   └─mustashe:::check_stash_dir()
   6.     └─base::tryCatch(...)
   7.       └─base tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
Note: found 50 marked UTF-8 strings
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Malformed Description field: should contain one or more complete sentences.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    23.2Mb
    models   1.1Mb
Note: found 47936 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 5 marked Latin-1 strings
  Note: found 7187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Note: found 140 marked UTF-8 strings
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  19.2Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 171.1Mb
  sub-directories of 1Mb or more:
    libs  170.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [27s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-ptd_create_ggplot.R:79:3'): it returns a ggplot object ───────
  p$labels (`actual`) not equal to list(...) (`expected`).
  
  `actual$title`:   "SPC Chart of Y, starting 01/01/2020"
  `expected$title`: "SPC Chart of Y, starting 02/01/2020"
  ── Failure ('test-ptd_create_ggplot.R:299:3'): it sets the main title correctly ──
  p1$labels$title (`actual`) not equal to "SPC Chart of Y, starting 02/01/2020" (`expected`).
  
  `actual`:   "SPC Chart of Y, starting 01/01/2020"
  `expected`: "SPC Chart of Y, starting 02/01/2020"
  
  [ FAIL 2 | WARN 733 | SKIP 3 | PASS 430 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.3Mb
    R              6.3Mb
    classic-bugs   1.5Mb
    include        5.7Mb
    libs          17.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ALL’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘nlraa’
  All declared Imports should be used.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Package suggested but not available for checking: ‘doMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'treeio', 'ggtree'
Package unavailable to check Rd xrefs: ‘treeio’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_i = a_i \, \mod 
                             \, m_i, \quad 1 \le i \le n 
l.560 ...i \, \mod \, m_i, \quad 1 \le i \le n }{}
                                                  
! Undefined control sequence.
<argument> a_i = a_j \, \mod 
                             \, \gcd (m_i, m_j)
l.564 \deqn{a_i = a_j \, \mod \, \gcd(m_i, m_j)}{}
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs  14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘oceanexplorer.Rmd’ using rmarkdown
Quitting from lines 133-134 (oceanexplorer.Rmd) 
Error: processing vignette 'oceanexplorer.Rmd' failed with diagnostics:
crs not found: is it missing?
--- failed re-building ‘oceanexplorer.Rmd’

SUMMARY: processing the following file failed:
  ‘oceanexplorer.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.0Mb
    libs   3.4Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 86.2Mb
  sub-directories of 1Mb or more:
    libs  85.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> [0,\text 
                    {min}(p_1,p_2))
l.75 a number in \eqn{[0,\text{min}(p_1,p_2))}{}
                                                , indicating the cross-secti...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  43.6Mb
GNU make is a SystemRequirements.
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.2Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.7Mb
Note: found 32 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Package suggested but not available for checking: ‘paintmap’
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/OpenCL.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.5Mb
GNU make is a SystemRequirements.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs   14.8Mb
    share  10.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
Note: found 2524 marked UTF-8 strings
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 201.2Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    data      1.4Mb
    libs    190.0Mb
    models    4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: ‘openNLPmodels.en’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Note: found 167 marked UTF-8 strings
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   1.3Mb
    libs      5.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.7Mb
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     34.9Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   6.2Mb
Note: found 263 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Package required but not available: ‘genbankr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dbplyr’ ‘downloadthis’ ‘ggExtra’ ‘htmlwidgets’ ‘methods’
  ‘rmarkdown’ ‘scales’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
Package required but not available: ‘heatmapFlex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/pastclim.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   2.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   2.8Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/pbdMPI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 106.8Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  103.3Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PythonInR’
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs    7.6Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ncvreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  14.7Mb
Note: found 7326 marked UTF-8 strings
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-founder-inbreeding.R:24:3'): setFounderInbreeding works on lists ──
  fi(y1) not equal to c(`1` = 1, `2` = 1, `4` = 1).
  3/3 mismatches (average diff: 1)
  [1] 0 - 1 == -1
  [2] 0 - 1 == -1
  [3] 0 - 1 == -1
  ── Failure ('test-founder-inbreeding.R:27:3'): setFounderInbreeding works on lists ──
  fi(y2) not equal to c(`1` = 0, `2` = 1, `4` = 0).
  1/3 mismatches
  [2] 0 - 1 == -1
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 588 ]
  Error: Test failures
  Execution halted
Note: found 6 marked UTF-8 strings
installed size is 108.6Mb
  sub-directories of 1Mb or more:
    libs  107.6Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package suggested but not available for checking: ‘ptmixed’
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   7.6Mb
Namespace in Imports field not imported from: ‘fixest’
  All declared Imports should be used.
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    libs  56.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Note: possible error in 'simplify2array(msg, except = 0L)': unused argument (except = 0) 
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/personalized.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
xgb_cv_personalized: possible error in simplify2array(msg, except =
  0L): unused argument (except = 0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘shinyWidgets’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.9Mb
Error(s) in re-building vignettes:
--- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown
Quitting from lines 280-281 (AdvancedFeatures.Rmd) 
Error: processing vignette 'AdvancedFeatures.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘AdvancedFeatures.Rmd’

--- re-building ‘Ancestral.Rmd’ using rmarkdown
Error: processing vignette 'Ancestral.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Ancestral.Rmd’

--- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown
Error: processing vignette 'IntertwiningTreesAndNetworks.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘IntertwiningTreesAndNetworks.Rmd’

--- re-building ‘MLbyHand.Rmd’ using rmarkdown
Error: processing vignette 'MLbyHand.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘MLbyHand.Rmd’

--- re-building ‘Morphological.Rmd’ using rmarkdown
Error: processing vignette 'Morphological.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Morphological.Rmd’

--- re-building ‘Networx.Rmd’ using rmarkdown
Error: processing vignette 'Networx.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Networx.Rmd’

--- re-building ‘Trees.Rmd’ using rmarkdown
Error: processing vignette 'Trees.Rmd' failed with diagnostics:
there is no package called ‘sass’
--- failed re-building ‘Trees.Rmd’

SUMMARY: processing the following files failed:
  ‘AdvancedFeatures.Rmd’ ‘Ancestral.Rmd’
  ‘IntertwiningTreesAndNetworks.Rmd’ ‘MLbyHand.Rmd’ ‘Morphological.Rmd’
  ‘Networx.Rmd’ ‘Trees.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
installed size is 43.9Mb
  sub-directories of 1Mb or more:
    libs  43.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘cowplot’ ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
at_trans : <anonymous>: no visible global function definition for
  ‘viewportTransform’
at_trans : <anonymous>: no visible global function definition for
  ‘groupShear’
at_trans : <anonymous>: no visible global function definition for
  ‘groupFlip’
grobCoords.pp_grobCoords: no visible global function definition for
  ‘emptyGrobCoords’
grobCoords.pp_ps_transformation: no visible global function definition
  for ‘emptyGrobCoords’
makeContent.pp_transformation: no visible global function definition
  for ‘defineGrob’
makeContent.pp_transformation: no visible global function definition
  for ‘useGrob’
transformationGrob: no visible binding for global variable
  ‘viewportTransform’
xylists_to_grobcoords: no visible global function definition for
  ‘emptyGrobCoords’
xylists_to_grobcoords: no visible global function definition for
  ‘gridCoords’
xylists_to_grobcoords : <anonymous>: no visible global function
  definition for ‘gridCoords’
xylists_to_grobcoords: no visible global function definition for
  ‘gridGrobCoords’
Undefined global functions or variables:
  defineGrob emptyGrobCoords gridCoords gridGrobCoords groupFlip
  groupShear useGrob viewportTransform
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2048 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
installed size is 25.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.6Mb
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installed size is 13.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
Note: found 7256 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
installed size is 55.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
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    data   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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installed size is  7.3Mb
  sub-directories of 1Mb or more:
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installed size is 19.4Mb
  sub-directories of 1Mb or more:
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installed size is 42.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-predict.R:12:3'): map.predict function works ─────────────────
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  ── Failure ('test-predict.R:13:3'): map.predict function works ─────────────────
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 42.6Mb
  sub-directories of 1Mb or more:
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installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \hat d:=\underset 
                             {|d|<0.5}{\mathrm {argmin}}\bigg \{\sum _{h=s}^...
l.88 ...d)}h^{2d-1}\bigg|^r\bigg\}, \quad r > 0}{}
                                                  .
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \to a}\fra...
l.269 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.271 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \rightarro...
l.469 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.472 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
installed size is 12.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
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installed size is 10.8Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
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    libs   8.9Mb
Namespace in Imports field not imported from: ‘here’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.963 ...m_{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1138 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1289 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 42966 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 165 marked UTF-8 strings
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   4.9Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
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    libs   8.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 64.8Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 82.3Mb
  sub-directories of 1Mb or more:
    libs  82.0Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
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Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘LambertW’ ‘gtools’ ‘mstate’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
Note: found 26 marked Latin-1 strings
Package required and available but unsuitable version: ‘splines’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    libs  48.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.1Mb
  sub-directories of 1Mb or more:
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installed size is  7.4Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘muscle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘sjPlot’
  All declared Imports should be used.
installed size is 47.1Mb
  sub-directories of 1Mb or more:
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Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘PUPAIM-Ex.R’ failed
The error most likely occurred in:

> ### Name: SSLangmuir1analysis
> ### Title: Langmuir Isotherm Nonlinear Analysis via selfStart and Langmuir
> ###   First Linear Model
> ### Aliases: SSLangmuir1analysis
> 
> ### ** Examples
> 
> Ce <- c(0.01353, 0.04648, 0.13239, 0.27714, 0.41600, 0.63607, 0.80435, 1.10327, 1.58223)
> Qe <- c(0.03409, 0.06025, 0.10622, 0.12842, 0.15299, 0.15379, 0.15735, 0.15735, 0.16607)
> SSLangmuir1analysis(Ce,Qe)
Error in (attr(object, "initial"))(mCall = mCall, data = data, LHS = LHS,  : 
  unused arguments (control = list(50, 1e-05, 0.0009765625, FALSE, FALSE, 0, FALSE), trace = FALSE)
Calls: SSLangmuir1analysis
Execution halted
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘lazyeval’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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Missing or unexported objects:
  ‘async::http_get’ ‘async::http_stop_for_status’ ‘async::synchronise’
  ‘async::when_all’
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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    libs         2.7Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 85.8Mb
  sub-directories of 1Mb or more:
    libs  85.2Mb
'LazyData' is specified without a 'data' directory
installed size is 98.6Mb
  sub-directories of 1Mb or more:
    libs  97.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
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Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘readxl’ ‘reshape2’ ‘sjmisc’ ‘stringr’ ‘xlsx’
  All declared Imports should be used.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
installed size is 38.4Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     33.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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installed size is 11.2Mb
  sub-directories of 1Mb or more:
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    contrib   3.7Mb
    doc       3.0Mb
    libs      1.3Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Note: found 4 marked UTF-8 strings
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.7Mb
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘psych’ ‘psychTools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc         2.9Mb
    shiny_app   1.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Package suggested but not available for checking: ‘slingshot’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   1.3Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets       10.0Mb
    super-tiny-icons   1.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    libs  59.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  10.1Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.0Mb
GNU make is a SystemRequirements.
Note: found 8 marked UTF-8 strings
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  38.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    libs  52.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26334 marked UTF-8 strings
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 62.1Mb
  sub-directories of 1Mb or more:
    libs  61.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘rlemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
    po    2.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rcplex.Rcheck/00install.out’ for details.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      2.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    include  44.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.8Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs          13.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      5.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rcrypt.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Hs.eg.db’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    data   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
Note: found 1036 marked UTF-8 strings
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      5.3Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Package required and available but unsuitable version: ‘EstimationTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6034 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  13.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     22.2Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Package suggested but not available for checking: ‘ccdata’
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 263.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    libs      255.5Mb
    pictures    1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Found the following significant warnings:
  Texture.cpp:244:22: warning: 'gluBuild2DMipmaps' is deprecated: first deprecated in macOS 10.9 - "Use glGenerateMipmap" [-Wdeprecated-declarations]
  Texture.cpp:257:24: warning: 'gluScaleImage' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rgl.Rcheck/00install.out’ for details.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    doc     2.4Mb
    fonts   1.5Mb
    libs   20.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/high-sierra-x86_64/results/4.1/ricu.Rcheck/vign_test/ricu/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See jss.log for more info.
--- failed re-building ‘jss.Rmd’

--- re-building ‘ricu.Rmd’ using rmarkdown
--- finished re-building ‘ricu.Rmd’

--- re-building ‘uom.Rmd’ using rmarkdown
--- finished re-building ‘uom.Rmd’

SUMMARY: processing the following file failed:
  ‘jss.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /Volumes/Builds/packages/high-sierra-x86_64/results/4.1/riot.Rcheck/00_pkg_src/riot/src/vtk-src/Common/DataModel/vtkCellTreeLocator.cxx:315:9: warning: field 'Cnt' will be initialized after field 'Min' [-Wreorder]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/riot.Rcheck/00install.out’ for details.
installed size is 174.0Mb
  sub-directories of 1Mb or more:
    extdata    5.4Mb
    libs     168.5Mb
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
'LazyData' is specified without a 'data' directory
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs     17.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.1Mb
'LazyData' is specified without a 'data' directory
installed size is 55.1Mb
  sub-directories of 1Mb or more:
    libs  54.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'reactome.db', 'fgsea'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    rmd   5.8Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RMark.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 108.7Mb
  sub-directories of 1Mb or more:
    libs  108.3Mb
GNU make is a SystemRequirements.
installed size is 68.7Mb
  sub-directories of 1Mb or more:
    libs  68.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs       1.1Mb
    minizinc   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is 40.6Mb
  sub-directories of 1Mb or more:
    libs  39.7Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 52.0Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
GNU make is a SystemRequirements.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘recount3’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Missing or unexported object: 'SummarizedExperiment::colnames'
Error(s) in re-building vignettes:
  ...
--- re-building ‘data.Rmd’ using rmarkdown
--- finished re-building ‘data.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 88-89 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error:
! 'colnames' is not an exported object from 'namespace:SummarizedExperiment'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘pbdMPI’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package unavailable to check Rd xrefs: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is 96.8Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     94.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  17.0Mb
Note: found 1 marked UTF-8 string
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Packages suggested but not available for checking:
  'affydata', 'illuminaHumanv3.db'
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RobLoxBioC.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’ ‘utils’
  All declared Imports should be used.
installed size is 66.1Mb
  sub-directories of 1Mb or more:
    libs  65.5Mb
GNU make is a SystemRequirements.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘Matrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
'LazyData' is specified without a 'data' directory
sh: cmake: command not found
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.5Mb
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
installed size is 54.0Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  47.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 93.8Mb
  sub-directories of 1Mb or more:
    libs  93.2Mb
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    dependencies  24.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/RSiena.Rcheck/00install.out’ for details.
Note: found 467 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    help   1.4Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 177.2Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.8Mb
    libs  170.1Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
GNU make is a SystemRequirements.
installed size is 246.6Mb
  sub-directories of 1Mb or more:
    lib    28.7Mb
    libs  215.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Namespaces in Imports field not imported from:
  ‘bitops’ ‘httpuv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is 94.5Mb
  sub-directories of 1Mb or more:
    libs  94.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R           1.3Mb
    bootstrap   1.6Mb
    doc         1.2Mb
    help        2.8Mb
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmarkdown   6.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs       2.1Mb
    projects   2.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data      3.4Mb
    extdata   1.4Mb
    libs      3.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.9Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  57.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘lubridate’ ‘rstantools’
  All declared Imports should be used.
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.3Mb
Package which this enhances but not available for checking: ‘glmmADMB’
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 65.0Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     59.6Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
    test   4.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  45.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs    8.1Mb
    yacas   1.3Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs    8.8Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 37 marked Latin-1 strings
  Note: found 172 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Note: found 63 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘Matrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  44.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.7Mb
Packages suggested but not available for checking: 'GO.db', 'org.Sc.sgd.db'
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.5Mb
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.3Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \dfrac 
                       
l.190 ...omputed by  \eqn{\dfrac{|I|-ec}{|I|-1}}{}
                                                  .
! Undefined control sequence.
<argument> 1 - \dfrac 
                      {\hat {\ell }_{k,n}(1_I,0_{I^c})}{|I|}
l.278 ...ac{\hat{\ell}_{k,n}(1_I,0_{I^c})}{|I|}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1276 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1362 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> \hat {S}_{I,k,n}=\dfrac 
                                   {\hat {D}_{I,k,n}}{\hat {D}_{k,n}}
l.1372 ...dfrac{\hat{D}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                  
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1605 ...hat{\Upsilon}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                   the empirical counterpart...
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1605 ...n{\dfrac{\Upsilon_I(\ell)}{D_I(\ell)}}{}
                                                  .
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ... by \eqn{\dfrac{(2|I|+2)!}{2(|I|!)^2}}{}
                                                  .
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following executable file:
  inst/extdata/Azores.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘Nebulosa’
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   3.2Mb
Packages suggested but not available for checking:
  'ontoProc', 'SingleCellSignalR'
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DuoClustering2018’
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocSingular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Nebulosa', 'infercnv', 'UCell', 'AUCell'
Package unavailable to check Rd xrefs: ‘infercnv’
Unknown package ‘UCell’ in Rd xrefs
Running ‘testthat.R’ [74s/76s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      color = color2)`: arguments imply differing number of rows: 5, 0
  Backtrace:
      ▆
   1. └─SCpubr::do_FunctionalAnnotationPlot(...) at test-do_FunctionalAnnotationPlot.R:5:4
   2.   └─SCpubr:::do_EnrichedTermTreePlot(...)
   3.     ├─enrichplot::treeplot(...)
   4.     └─enrichplot::treeplot(...)
   5.       └─enrichplot:::treeplot.enrichResult(...)
   6.         └─enrichplot:::group_tree(...)
   7.           └─enrichplot:::add_cladelab(...)
   8.             └─base::data.frame(...)
  
  [ FAIL 1 | WARN 0 | SKIP 417 | PASS 87 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions:
  'S4Vectors', 'SummarizedExperiment', 'SingleCellExperiment', 'edgeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.5Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    libs  58.3Mb
Package unavailable to check Rd xrefs: ‘INLA’
Found the following executable file:
  inst/shape/GermanyNUTS3.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
Note: found 3 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  15.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.7Mb
Package suggested but not available for checking: ‘rsbml’
Package suggested but not available for checking: ‘ArrayExpress’
Package unavailable to check Rd xrefs: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.5Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs    20.8Mb
    models   1.6Mb
Note: found 836 marked UTF-8 strings
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
Note: found 3128 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 52 marked UTF-8 strings
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘airway’
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   7.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 278.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    libs    272.1Mb
    sqlite    1.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘tripack’
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   4.9Mb
Found the following executable files:
  inst/extdata/access.dbf
  inst/extdata/existing.dbf
  inst/extdata/existingna.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> X \in \mathbb 
                         {R}{n\times p}
l.3262 ...data \eqn{X \in \mathbb{R}{n\times p}}{}
                                                   such that its rows are
! Undefined control sequence.
<argument> ...Delta _{p-1} =\lbrace z \in \mathbb 
                                                  {R}^p~|~z_j > 0, \sum _{i=...
l.3265 }{}
           test whether the data is uniformly distributed.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package required and available but unsuitable version: ‘GenomeInfoDb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SimInf.Rnw’ using Sweave
--- finished re-building 'SimInf.Rnw'

--- re-building ‘scheduled-events.Rmd’ using rmarkdown
Error: processing vignette 'scheduled-events.Rmd' failed with diagnostics:
there is no package called 'vctrs'
--- failed re-building ‘scheduled-events.Rmd’

SUMMARY: processing the following file failed:
  ‘scheduled-events.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  12.3Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.5Mb
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Package required but not available: ‘qpgraph’

Packages suggested but not available for checking: 'clipper', 'topologyGSA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  20.7Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.0Mb
GNU make is a SystemRequirements.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘gurobi’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Note: found 1122 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.3Mb
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘snapKrig-Ex.R’ failed
The error most likely occurred in:

> ### Name: Math.sk
> ### Title: Math group generics
> ### Aliases: Math.sk
> 
> ### ** Examples
> 
> g = sk_validate(list(gval=stats::rnorm(4^2), gdim=4, gres=0.5))
> summary(g)
complete sk grid
16 points
range [-2.21, 1.60]
..............................
Error in sk_make(g) : argument gdim not found
Calls: summary ... summary.sk -> apply -> sk_coords -> sk -> sk_validate -> sk_make
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘snapKrig_introduction.Rmd’ using rmarkdown
Quitting from lines 60-67 (snapKrig_introduction.Rmd) 
Error: processing vignette 'snapKrig_introduction.Rmd' failed with diagnostics:
argument gdim not found
--- failed re-building ‘snapKrig_introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘snapKrig_introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.8Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘itertools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.1Mb
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘sos.Rnw’ using Sweave
Loading required package: brew

Attaching package: 'sos'

The following object is masked from 'package:utils':

    ?


Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.0Mb
Package suggested but not available for checking: ‘r2cytoscape’
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  13.0Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.9Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    libs  36.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is 55.8Mb
  sub-directories of 1Mb or more:
    libs  54.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
Note: found 283 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.0Mb
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   9.7Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
Note: found 34 marked UTF-8 strings
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
Found the following executable files:
  inst/extdata/SouthernBuh-habitats_shapefile.dbf
  inst/extdata/test_shapefile.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Note: found 189 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘MASS’ ‘psy’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is 17.4Mb
  sub-directories of 1Mb or more:
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    extdata   2.6Mb
    libs     12.4Mb
'LazyData' is specified without a 'data' directory
Note: found 7587 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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installed size is 51.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs  10.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  26.2Mb
'LazyData' is specified without a 'data' directory
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    libs  68.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Note: found 40748 marked UTF-8 strings
installed size is 29.3Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    libs  51.8Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       1.8Mb
installed size is 69.0Mb
  sub-directories of 1Mb or more:
    libs  68.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> ### Name: mdim
> ### Title: Read or write data using GDAL's multidimensional array API
> ### Aliases: mdim read_mdim write_mdim
> 
> ### ** Examples
> 
> set.seed(135)
> m = matrix(runif(10), 2, 5)
> names(dim(m)) = c("stations", "time")
> times = as.Date("2022-05-01") + 1:5
> pts = st_as_sfc(c("POINT(0 1)", "POINT(3 5)"))
> s = st_as_stars(list(Precipitation = m)) |>
+  st_set_dimensions(1, values = pts) |>
+  st_set_dimensions(2, values = times)
> nc = tempfile(fileext=".nc")
> if (compareVersion(sf_extSoftVersion()["GDAL"], "3.4.0") > -1) {
+   write_mdim(s, nc)
+   # try ncdump on the generated file
+   print(read_mdim(nc))
+ }
Error: cannot open driver
Execution halted
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 18 marked UTF-8 strings
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.3Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
Note: found 20 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Package required but not available: ‘pvca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.6Mb
Package suggested but not available for checking: ‘INLA’
installed size is 66.9Mb
  sub-directories of 1Mb or more:
    libs  65.8Mb
Data codoc mismatches from documentation object 'SLCS':
Variables in data frame 'SLCS'
  Code: SLCS_1 SLCS_10 SLCS_11 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
  Docs: SLCS_11 SLCS_1 SLCS_10 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.6Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.3Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.3Mb
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installed size is  9.5Mb
  sub-directories of 1Mb or more:
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Note: found 83 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    doc    3.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...! \perp T_1 | \tilde {S}_1 \; \text 
                                                  {and} \; \tilde {S}_1 \per...
l.3471 ...perp \!\!\! \perp T_0 | \tilde{S}_0 .}{}
                                                   This can informally be
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   1.5Mb
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.5Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    libs  49.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  39.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘udunits2’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    fonts   1.7Mb
    libs   16.0Mb
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 81 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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    libs   4.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 301 marked UTF-8 strings
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘biblio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dearseq’
Package unavailable to check Rd xrefs: ‘dearseq’
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    libs  40.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    apps   2.3Mb
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      2.0Mb
    telemac   1.0Mb
Package suggested but not available for checking: ‘INLA’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [112s/112s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_MasterEstim.R:8:3'): TemperedEstim_with_Classic_ML_gives_correct_return ──
  round(TestObject@par[["lambda -"]], digits = 4) (`actual`) not equal to 1.3832 (`expected`).
  
    `actual`: 1.3833
  `expected`: 1.3832
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_MasterEstim.R:8:2
   2. │ └─base::withCallingHandlers(...)
   3. └─testthat::expect_equal(...) at test_MasterEstim.R:18:4
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 289 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 311.1Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs  307.8Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.8Mb
    tessdata  14.1Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.0Mb
    libs   4.1Mb
Missing or unexported object: ‘Matrix::rowScale’
Running examples in ‘text2vec-Ex.R’ failed
The error most likely occurred in:

> ### Name: BNS
> ### Title: BNS
> ### Aliases: BNS
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("movie_review")
> N = 1000
> it = itoken(head(movie_review$review, N), preprocessor = tolower, tokenizer = word_tokenizer)
> vocab = create_vocabulary(it)
> dtm = create_dtm(it, vocab_vectorizer(vocab))
as(<dgTMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead
> model_bns = BNS$new()
> dtm_bns = model_bns$fit_transform(dtm, head(movie_review$sentiment, N))
Error: 'colScale' is not an exported object from 'namespace:Matrix'
Execution halted
Running ‘testthat.R’ [32s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   7. │     └─text2vec::normalize(x_internal, private$norm)
   8. └─base::.handleSimpleError(...)
   9.   └─base (local) h(simpleError(msg, call))
  ── Error ('test-s3-interface.R:41:3'): S3 bns ──────────────────────────────────
  Error: 'colScale' is not an exported object from 'namespace:Matrix'
  Backtrace:
      ▆
   1. ├─mlapi::fit_transform(dtm, bns, y) at test-s3-interface.R:41:2
   2. └─mlapi:::fit_transform.Matrix(dtm, bns, y)
   3.   └─model$fit_transform(x, y = y, ...)
   4.     └─self$transform(x, ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 80 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘files-multicore.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'files-multicore.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘files-multicore.Rmd’

--- re-building ‘glove.Rmd’ using rmarkdown
--- finished re-building ‘glove.Rmd’

--- re-building ‘text-vectorization.Rmd’ using rmarkdown
Quitting from lines 280-281 (text-vectorization.Rmd) 
Error: processing vignette 'text-vectorization.Rmd' failed with diagnostics:
'rowScale' is not an exported object from 'namespace:Matrix'
--- failed re-building ‘text-vectorization.Rmd’

SUMMARY: processing the following file failed:
  ‘text-vectorization.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_{i} - \text 
                         {min}(\mathbf {x})
l.447 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> \text 
                 {max}(\mathbf {x}) - \text {min}(\mathbf {x})
l.447 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> \text {max}(\mathbf {x}) - \text 
                                            {min}(\mathbf {x})
l.447 ...(\mathbf{x}) - \text{min}(\mathbf{x})}}{}
                                                  
! Undefined control sequence.
<argument> x_{i} - \text 
                         {median}(\mathbf {x})
l.654 ...\mathbf{x})/{1.35}}\right)\right]^{-1}}{}
                                                  
! Undefined control sequence.
<argument> \text 
                 {IQR}(\mathbf {x})/{1.35}
l.654 ...\mathbf{x})/{1.35}}\right)\right]^{-1}}{}
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    libs  47.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’ ‘tidybins’ ‘validata’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘motivation.md’ using mdweave_to_html
Cannot find pandoc. Not able to weave vignette.
Error: processing vignette 'motivation.md' failed with diagnostics:
Failed to locate ‘weave’ output file ‘motivation.pdf’ or ‘motivation.html’ for vignette with name ‘motivation’ and engine ‘simplermarkdown::mdweave_to_html’. The following files exist in working directory ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/tidyCpp.Rcheck/vign_test/tidyCpp/vignettes’: ‘motivation.md’ (18115 bytes), ‘water.css’ (1193 bytes)
--- failed re-building ‘motivation.md’

SUMMARY: processing the following file failed:
  ‘motivation.md’

Error: Vignette re-building failed.
Execution halted
Note: found 40 marked UTF-8 strings
Note: found 4546 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   4.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs    13.5Mb
    tiledb  31.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.965 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.965 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   D
l.965 visjs documentation}}
                           .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1021 visjs documentation}}
                            .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1021 visjs documentation}}
                            .
! Illegal parameter number in definition of \Hy@tempa.
<to be read again> 
                   g
l.1021 visjs documentation}}
                            .
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  45.5Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    3.6Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 177.5Mb
  sub-directories of 1Mb or more:
    R          5.2Mb
    help       1.6Mb
    include    1.5Mb
    libs     168.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix
Loading required package: fds
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl

Attaching package: 'fda'

The following object is masked from 'package:graphics':

    matplot

--- finished re-building 'trackeR.Rnw'

SUMMARY: processing the following file failed:
  ‘TourDetrackeR.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
'LazyData' is specified without a 'data' directory
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  49.5Mb
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   2.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.1Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata  14.8Mb
installed size is 102.7Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs  97.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs  66.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       23.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   4.3Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
'LazyData' is specified without a 'data' directory
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls not declared from:
  ‘unitizerdummypkg1’ ‘unitizerdummypkg2’
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  42.8Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 7872 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
Note: found 1 marked UTF-8 string
Note: found 33 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  24.5Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 262.8Mb
  sub-directories of 1Mb or more:
    extdata    2.7Mb
    libs     258.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘taxlist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   3.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  55.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.0Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 56.1Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
Note: found 4954 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 69.1Mb
  sub-directories of 1Mb or more:
    libs  67.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   5.5Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1668 marked UTF-8 strings
Running ‘testthat.R’ [15s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(wdnet)
  > 
  > test_check("wdnet")
  
   *** caught segfault ***
  address 0x10e761a30, cause 'memory not mapped'
  An irrecoverable exception occurred. R is aborting now ...
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.4Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.6Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    bin   4.2Mb
    lib   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.0Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    java  24.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Package suggested but not available for checking: ‘SDMTools’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.md' using mdweave_to_html
Evaluating code in inline block '<unlabeled inline block>'.
Evaluating code in block 'load_package'.
Evaluating code in block 'loading_data'.
Evaluating code in block 'first_example'.
Evaluating code in block 'cumulate_formula'.
Evaluating code in block 'derive_sbi_levels'.
Evaluating code in block 'accumulate_formula'.
Evaluating code in block 'dataframe_construction'.
Evaluating code in block 'dataframe_cumulate'.
Evaluating code in block 'helpers'.
Evaluating code in block 'smoketest1'.
Evaluating code in block 'smoketest2'.
Evaluating code in block 'smoketest3'.
Error: processing vignette 'introduction.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'introduction.md'

SUMMARY: processing the following file failed:
  'introduction.md'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Running examples in 'ACEP-Ex.R' failed
The error most likely occurred in:

> ### Name: acep_clean
> ### Title: Limpieza de texto.
> ### Aliases: acep_clean
> ### Keywords: normalizacion
> 
> ### ** Examples
> 
> acep_clean("El SUTEBA fue al paro. Reclaman mejoras salariales.", rm_cesp = FALSE)
Warning in readRDS(url("https://observatoriodeconflictividad.org/basesdatos/tildes.rds")) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in readRDS(url("https://observatoriodeconflictividad.org/basesdatos/tildes.rds")) : 
  cannot open the connection
Calls: acep_clean -> tryCatch -> tryCatchList -> readRDS
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       2.0Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:226:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct std::pair<CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Fixed_alpha_shape_cell_base_3<CGAL::Epick, CGAL::Delaunay_triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Fixed_alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Fixed_alpha_shape_cell_base_3<CGAL::Epick> > > > > >, CGAL::Default, CGAL::Default, CGAL::Default>, false>, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.1/BH/include/boost/container/detail/copy_move_algo.hpp:226:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct std::pair<CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Delaunay_triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Default, CGAL::Default, CGAL::Default>, false>, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.1/AlphaHull3D.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.0Mb
Package suggested but not available for checking: 'metaboliteIDmapping'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.8Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.1Mb
    testdata   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.2Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'AquaBEHER.Rmd' using rmarkdown
Error: processing vignette 'AquaBEHER.Rmd' failed with diagnostics:
Using anchor_sections requires Pandoc 2.0+
--- failed re-building 'AquaBEHER.Rmd'

SUMMARY: processing the following file failed:
  'AquaBEHER.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Error(s) in re-building vignettes:
--- re-building 'archeofrag-vignette.Rmd' using rmarkdown
Error: processing vignette 'archeofrag-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 5
--- failed re-building 'archeofrag-vignette.Rmd'

SUMMARY: processing the following file failed:
  'archeofrag-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 71.9Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs  67.2Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      2.1Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    bin   22.9Mb
    misc   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'asteRiskData'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.2Mb
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/augmentedRCBD.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'autoReg-Ex.R' failed
The error most likely occurred in:

> ### Name: ggcmprsk
> ### Title: Draw Cumulative Incidence Curves for Competing Risks
> ### Aliases: ggcmprsk
> 
> ### ** Examples
> 
> data(melanoma,package="boot")
> melanoma$status1 = ifelse(melanoma$status==1,1,ifelse(melanoma$status==2,0,2))
> ggcmprsk(time/365+status1~1,data=melanoma)
Error in `mold_formula_default_process_outcomes()`:
! Interaction terms can't be specified on the LHS of `formula`.
i The following interaction term was found: `time/365`.
Backtrace:
     x
  1. \-autoReg::ggcmprsk(time/365 + status1 ~ 1, data = melanoma)
  2.   +-base::suppressWarnings(...)
  3.   | \-base::withCallingHandlers(...)
  4.   +-tidycmprsk::cuminc(as.formula(formula), data = data, ...)
  5.   \-tidycmprsk:::cuminc.formula(...)
  6.     +-hardhat::mold(formula, data, blueprint = hardhat::default_formula_blueprint(intercept = TRUE))
  7.     \-hardhat:::mold.formula(formula, data, blueprint = hardhat::default_formula_blueprint(intercept = TRUE))
  8.       +-hardhat::run_mold(blueprint, data = data)
  9.       \-hardhat:::run_mold.default_formula_blueprint(blueprint, data = data)
 10.         \-hardhat:::mold_formula_default_process(...)
 11.           \-hardhat:::mold_formula_default_process_outcomes(blueprint = blueprint, data = data)
 12.             \-hardhat:::check_no_interactions(formula)
 13.               \-hardhat:::expr_check_no_interactions(expr, error_call = error_call)
 14.                 \-hardhat:::expr_check_no_interactions(expr[[i]], error_call = error_call)
 15.                   \-hardhat:::expr_check_no_interactions(expr[[i]], error_call = error_call)
 16.                     \-cli::cli_abort(message, call = error_call)
 17.                       \-rlang::abort(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Automatic_Regression_Modeling.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'Automatic_Regression_Modeling.Rmd'

--- re-building 'Bootstrap_Prediction.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'Bootstrap_Prediction.Rmd'

--- re-building 'Getting_started.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'Getting_started.Rmd'

--- re-building 'Statiastical_test_in_gaze.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'Statiastical_test_in_gaze.Rmd'

--- re-building 'Survival.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
Quitting from lines 195-196 (Survival.Rmd) 
Error: processing vignette 'Survival.Rmd' failed with diagnostics:
Interaction terms can't be specified on the LHS of `formula`.
i The following interaction term was found: `time/365`.
--- failed re-building 'Survival.Rmd'

SUMMARY: processing the following file failed:
  'Survival.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Running examples in 'avidaR-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_seq_into_org
> ### Title: Converts a genome instruction sequence into a digital organism
> ###   file
> ### Aliases: convert_seq_into_org
> 
> ### ** Examples
> 
> 
> # Create triplestore object
> triplestore <- triplestore_access$new()
> 
> # Set access options
> triplestore$set_access_options(
+   url = "https://graphdb.fortunalab.org",
+   user = "public_avida",
+   password = "public_avida",
+   repository = "avidaDB_test"
+ )
Initiating curl with CURL_SSL_BACKEND: openssl
Error: Server responded with status code '523 - unknown':
- Please, try in a few minutes.
- If error persists, please contact server administrator.
Execution halted
installed size is 57.9Mb
  sub-directories of 1Mb or more:
    libs  57.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'lixoftConnectors'
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(badger)
  > 
  > test_check("badger")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  
  == Failed tests ================================================================
  -- Error ('test-badges.R:90:3'): Other badges output as expected ---------------
  Error in `file(con, "r")`: cannot open the connection
  Backtrace:
      x
   1. +-testthat::expect_equal(...) at test-badges.R:90:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-badger::badge_sci_citation(...)
   5.   +-base::suppressWarnings(readLines(url))
   6.   | \-base::withCallingHandlers(...)
   7.   \-base::readLines(url)
   8.     \-base::file(con, "r")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'baffle.Rmd' using rmarkdown
Quitting from lines 88-95 (baffle.Rmd) 
Error: processing vignette 'baffle.Rmd' failed with diagnostics:
unused arguments (title.font = 2, title.cex = 1.5)
--- failed re-building 'baffle.Rmd'

SUMMARY: processing the following file failed:
  'baffle.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bartcs.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
NB: this package is only installed for sub-architecture 'x64'
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bayesdfa.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.7Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/BayesianPlatformDesignTimeTrend.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.7Mb
GNU make is a SystemRequirements.
NeedsCompilation field should likely be 'yes'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.9Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.3Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.3Mb
    libs      2.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   5.5Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bellreg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    help   1.1Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
installed size is 154.8Mb
  sub-directories of 1Mb or more:
    include  153.8Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/biblio.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.2Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bigstatsr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package which this enhances but not available for checking: 'asreml'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      2.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'blandr-Ex.R' failed
The error most likely occurred in:

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       6.6Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.9Mb
    libs      2.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bmgarch.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   3.8Mb
NB: this package is only installed for sub-architecture 'x64'
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 70.0Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
    lib      59.4Mb
GNU make is a SystemRequirements.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running examples in 'Boov-Ex.R' failed
The error most likely occurred in:

> ### Name: qsqrt
> ### Title: Rational approximation of square roots
> ### Aliases: qsqrt qsqrt2 qsqrt3 qsqrtPhi print.qsqrt
> 
> ### ** Examples
> 
> library(Boov)
> qsqrt(2, 7)
Big Rational ('bigq') :
[1] 239/169
attr("error")[1] 1.237894e-05
> qsqrt2(7)
Big Rational ('bigq') :
[1] 1583919189857867/1120000000000000
attr("error")[1] 2.220446e-16
> qsqrt3(22)
Big Rational ('bigq') :
[1] 3424893166652041261603462749599417/1977362991712265726655870271488000
attr("error")[1] 0
> qsqrtPhi(17)
Big Rational ('bigq') :
[1] 4110816771645448828103217812107/2540624486400000000000000000000
attr("error")[1] 1.332268e-15
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.88 0.18 6.6 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'boxfilter.Rmd' using rmarkdown
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

Error: processing vignette 'boxfilter.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/boxfilter.Rcheck/vign_test/boxfilter/vignettes/boxfilter.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See boxfilter.log for more info.
--- failed re-building 'boxfilter.Rmd'

SUMMARY: processing the following file failed:
  'boxfilter.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/brglm2.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.5Mb
Package suggested but not available for checking: 'glmmADMB'
Initiating curl with CURL_SSL_BACKEND: openssl
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    help   1.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    fonts   3.1Mb
    lib     4.6Mb
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running examples in 'bubbleHeatmap-Ex.R' failed
The error most likely occurred in:

> ### Name: bubbleHMLegends
> ### Title: Build Legend Trees for bubbleHeatmap Plots
> ### Aliases: bubbleHMLegends
> 
> ### ** Examples
> 
> legends <- bubbleHMLegends(
+   sizeBreaks = seq(0, 80, 10), colorBreaks = seq(-2, 2, 0.5), diameter = 0.8,
+   context = gpar(cex = 0.8), colorSeq = c("#053061", "#2166AC", "#4393C3", "#92C5DE", "#D1E5F0",
+   "#FDDBC7", "#F4A582", "#D6604D", "#B2182B", "#67001F"), unitBase = unit(0.5, "cm"),
+   legendHeight = 9, legendTitles = c("Estimate", "NegLog10P"))
> grid.draw(legends)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
Error(s) in re-building vignettes:
--- re-building 'GEO_App.Rmd' using rmarkdown
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178620&format=file&file=GSE178620%5Fraw%5Fabundances%2Ecsv%2Egz'
Quitting from lines 60-67 (GEO_App.Rmd) 
Error: processing vignette 'GEO_App.Rmd' failed with diagnostics:
cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178620&format=file&file=GSE178620%5Fraw%5Fabundances%2Ecsv%2Egz'
--- failed re-building 'GEO_App.Rmd'

--- re-building 'IntegratingMultiomics.Rmd' using rmarkdown
--- finished re-building 'IntegratingMultiomics.Rmd'

--- re-building 'bulkAnalyseR.Rmd' using rmarkdown
--- finished re-building 'bulkAnalyseR.Rmd'

SUMMARY: processing the following file failed:
  'GEO_App.Rmd'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/bws.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc        2.1Mb
    pictures   4.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/CARME.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'cmp_rsk_RHC.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
Quitting from lines 88-90 (cmp_rsk_RHC.Rmd) 
Error: processing vignette 'cmp_rsk_RHC.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'cmp_rsk_RHC.Rmd'

SUMMARY: processing the following file failed:
  'cmp_rsk_RHC.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'CausalGPS-Ex.R' failed
The error most likely occurred in:

> ### Name: set_logger
> ### Title: Set Logger Settings
> ### Aliases: set_logger
> 
> ### ** Examples
> 
> 
> set_logger("Debug")
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  18.62 1.25 25.5 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   1.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
GNU make is a SystemRequirements.
Running examples in 'cbsodataR-Ex.R' failed
The error most likely occurred in:

> ### Name: cbs_get_catalogs
> ### Title: Retrieves the possible catalog values that can be used for
> ###   retrieving data
> ### Aliases: cbs_get_catalogs
> 
> ### ** Examples
> 
> catalogs <- cbs_get_catalogs()
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Warning: Failing: http://opendata.cbs.nl/ODataCatalog/Tables?$format=json
Retrying...
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: cbs_get_catalogs ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'cdcfluview-Ex.R' failed
The error most likely occurred in:

> ### Name: hospitalizations
> ### Title: Laboratory-Confirmed Influenza Hospitalizations
> ### Aliases: hospitalizations
> 
> ### ** Examples
> 
> hosp_fs <- hospitalizations("flusurv", years=2015)
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: hospitalizations ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Running 'test-all.R' [5s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("cdcfluview")
  Loading required package: cdcfluview
  Initiating curl with CURL_SSL_BACKEND: openssl
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 1 ]
  
  == Skipped tests ===============================================================
  * On CRAN (1)
  
  == Failed tests ================================================================
  -- Error ('test-cdcfluview.R:7:3'): New API works ------------------------------
  Error in `open.connection(con, "rb")`: cannot open the connection
  Backtrace:
       x
    1. +-testthat::expect_that(geographic_spread(years = 2017), is_a("data.frame")) at test-cdcfluview.R:7:2
    2. | \-testthat (local) condition(object)
    3. |   \-testthat::expect_is(x, class)
    4. |     \-testthat::quasi_label(enquo(object), label, arg = "object")
    5. |       \-rlang::eval_bare(expr, quo_get_env(quo))
    6. \-cdcfluview::geographic_spread(years = 2017)
    7.   \-jsonlite::fromJSON("https://gis.cdc.gov/grasp/Flu8/GetPhase08InitApp?appVersion=Public")
    8.     \-jsonlite:::parse_and_simplify(...)
    9.       \-jsonlite:::parseJSON(txt, bigint_as_char)
   10.         \-jsonlite:::parse_con(txt, bigint_as_char)
   11.           +-base::open(con, "rb")
   12.           \-base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 1 ]
  Error: Test failures
  Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'CirceR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.2Mb
    libs   3.4Mb
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/cgalMeshes.Rcheck/00install.out' for details.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'countreg'
Initiating curl with CURL_SSL_BACKEND: openssl
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char ï»¿ (U+FEFF)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char ï»¿ (U+FEFF)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clinUtils)
  > 
  > test_check("clinUtils")
  Initiating curl with CURL_SSL_BACKEND: openssl
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 301 ]
  
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Failure ('test_knitPrintListPlots.R:196:7'): A list of interactive table objects (flextable) is correctly included --
  grep("class=\"tabwid\"", outputHTMLFt) has length 0, not length 2.
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 301 ]
  Error: Test failures
  Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...{C}=c\mathbf {U}\cdot \operatorname 
                                                  {diag}(\mathbf {s}) + \mat...
l.147 \mathbf{1}\,\mathbf{o}^T}{}
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'cmfrec-Ex.R' failed
The error most likely occurred in:

> ### Name: CMF.from.model.matrices
> ### Title: Create a CMF model object from fitted matrices
> ### Aliases: CMF.from.model.matrices
> 
> ### ** Examples
> 
> ### Example 'adopting' a model from 'recosystem'
> library(cmfrec)
> library(recosystem)
> library(recommenderlab)
Loading required package: Matrix
Loading required package: arules

Attaching package: 'arules'

The following objects are masked from 'package:base':

    abbreviate, write

Loading required package: proxy

Attaching package: 'proxy'

The following object is masked from 'package:Matrix':

    as.matrix

The following objects are masked from 'package:stats':

    as.dist, dist

The following object is masked from 'package:base':

    as.matrix

> library(MatrixExtra)
Error: package 'MatrixExtra' is not installed for 'arch = i386'
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/collapse.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
! Missing $ inserted.
<inserted text> 
                $
l.2248 g(\gamma
               \_0) = -\log Z(\lambda, e\^{}\{\gamma\_0\}) ) and its first and 

Try to find the following text in d:/RCompile/CRANpkg/local/4.1/COMPoissonReg.Rcheck/vign_test/COMPoissonReg/vignettes/vignette.Rmd:
  g(\gamma 

You may need to add $ $ around a certain inline R expression `r ` in d:/RCompile/CRANpkg/local/4.1/COMPoissonReg.Rcheck/vign_test/COMPoissonReg/vignettes/vignette.Rmd (see the above hint). See https://github.com/rstudio/rmarkdown/issues/385 for more info.
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/COMPoissonReg.Rcheck/vign_test/COMPoissonReg/vignettes/vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette.log for more info.
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/conStruct.Rcheck/00install.out' for details.
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'quickstart.Rmd'

SUMMARY: processing the following file failed:
  'quickstart.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(coreCollection)
  > 
  > test_check("coreCollection")
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ProData'
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.3Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/crosstable.Rcheck/00install.out' for details.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ctsem.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
cci.nostrat: no visible global function definition for 'quantile'
cci.nostrat: no visible global function definition for 'axis'
cci.nostrat: no visible global function definition for 'lines'
cci.nostrat: no visible global function definition for 'legend'
cci.strat: no visible global function definition for 'axis'
cci.strat: no visible global function definition for 'lines'
cci.strat: no visible global function definition for 'legend'
clfs.nostrat: no visible global function definition for 'quantile'
clfs.nostrat: no visible global function definition for 'axis'
clfs.nostrat: no visible global function definition for 'lines'
clfs.nostrat: no visible global function definition for 'legend'
clfs.strat: no visible global function definition for 'axis'
clfs.strat: no visible global function definition for 'lines'
clfs.strat: no visible global function definition for 'legend'
pvals.2cat: no visible global function definition for 'pchisq'
pvals.cat: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    deps  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs    1.4Mb
    tests   1.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package required and available but unsuitable version: 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dblog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11145 (sockconn)
Execution halted
Package suggested but not available for checking: 'doMC'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [156s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(deepdep)
  > 
  > test_check("deepdep")
  Initiating curl with CURL_SSL_BACKEND: openssl
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 45 ]
  
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Error ('test-deepdep.R:32:3'): obtaining Bioc dependencies returns objects of correct types --
  Error in `value[[3L]](cond)`: les is not available neither on CRAN nor on Bioconductor
  Backtrace:
      x
   1. +-vcr::use_cassette(...) at test-deepdep.R:32:2
   2. | \-cassette$call_block(...)
   3. \-deepdep (local) deepdep_wrapped(...) at test-deepdep.R:33:4
   4.   \-base::tryCatch(...) at test-deepdep.R:3:2
   5.     \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.       \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.         \-value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 45 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: found non-ASCII strings
  'SRP05673: monocyte derived macrophages. none vs bacillus Calmette-Gu<c3><83><c2><a9>rin' in object 'DEET_example_data'
  'treated with: 100 nM 17<c3><9f>-estradiol + 25 ng/mL TNFa for 40min:3' in object 'DEET_example_data'
  'treated with: 100 nM 17<c3><9f>-estradiol (E2) for 40min:3' in object 'DEET_example_data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-portable flags in variable 'PKG_FFLAGS':
  -std=f2008
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/delaunay.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'demcon-Ex.R' failed
The error most likely occurred in:

> ### Name: get_cce
> ### Title: Retrieve Chronology of Constitutional Events Dataset
> ### Aliases: get_cce
> 
> ### ** Examples
> 
> 
> cce<-get_cce(del_file=TRUE, write_out = FALSE)
Initiating curl with CURL_SSL_BACKEND: openssl
trying URL 'https://comparativeconstitutionsproject.org/data/ccpcce_v1_3.zip'
Warning in utils::download.file(cce_url, file.path(tempdir(), "ccpcce_v1_3.zip")) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in utils::download.file(cce_url, file.path(tempdir(), "ccpcce_v1_3.zip")) : 
  cannot open URL 'https://comparativeconstitutionsproject.org/data/ccpcce_v1_3.zip'
Calls: get_cce -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
Package suggested but not available for checking: 'Rdonlp2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.5Mb
    libs   2.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/dexter.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/dfpk.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'rlibkriging'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'sha1.md' using mdweave_to_html
Evaluating code in block 'faq7_31'.
Evaluating code in block 'faq7_31digest'.
Evaluating code in block 'sha1_lm_sum'.
Evaluating code in block 'sha1_lm'.
Error: processing vignette 'sha1.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'sha1.md'

SUMMARY: processing the following file failed:
  'sha1.md'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'library' or 'require' calls not declared from:
  'MASS' 'Matrix' 'NNMF' 'RANN' 'RSpectra' 'c' 'coRanking' 'ggplot'
  'igraph' 'loe' 'scales' 'tidyr'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'library' or 'require' calls not declared from:
  'keras' 'reticulate' 'tensorflow' 'vegan'
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    include  15.5Mb
    libs      1.8Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Found the following significant warnings:

  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
  Warning: 'rgl::rgl.clear' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Error(s) in re-building vignettes:
--- re-building 'CombiningDratAndTravis.md' using mdweave_to_html
Error: processing vignette 'CombiningDratAndTravis.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'CombiningDratAndTravis.md'

--- re-building 'DratFAQ.md' using mdweave_to_html
Error: processing vignette 'DratFAQ.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'DratFAQ.md'

--- re-building 'DratForPackageAuthors.md' using mdweave_to_html
Error: processing vignette 'DratForPackageAuthors.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'DratForPackageAuthors.md'

--- re-building 'DratForPackageUsers.md' using mdweave_to_html
Error: processing vignette 'DratForPackageUsers.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'DratForPackageUsers.md'

--- re-building 'DratStepByStep.md' using mdweave_to_html
Error: processing vignette 'DratStepByStep.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'DratStepByStep.md'

--- re-building 'WhyDrat.md' using mdweave_to_html
Error: processing vignette 'WhyDrat.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'WhyDrat.md'

SUMMARY: processing the following files failed:
  'CombiningDratAndTravis.md' 'DratFAQ.md' 'DratForPackageAuthors.md'
  'DratForPackageUsers.md' 'DratStepByStep.md' 'WhyDrat.md'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    tutorials   5.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/dsfa.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dsBaseClient'
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.5Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.7Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
'LazyData' is specified without a 'data' directory
installed size is 43.9Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.4Mb
Package suggested but not available for checking: 'cmdstanr'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   7.3Mb
Package unavailable to check Rd xrefs: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   1.2Mb
Codoc mismatches from documentation object 'IQLearnFS_VHet-methods':
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   2.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  whv.c:62:18: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.1/eaf.Rcheck/00install.out' for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    bin       7.3Mb
    extdata   1.7Mb
    libs      2.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Title: Trim and Format Address Information
> ### Aliases: trim_address
> 
> ### ** Examples
> 
> addr_string <- " 2 Dept of Urology, Feinberg School of Medicine," 
> addr_string <- paste(addr_string, "Chicago, US; Dept of Mol Bio as well...")
> print(addr_string)
[1] " 2 Dept of Urology, Feinberg School of Medicine, Chicago, US; Dept of Mol Bio as well..."
> print(trim_address(addr = addr_string))
[1] "Dept of Urology, Feinberg School of Medicine, Chicago, US"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.8 0.47 500.6 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'econet.tex' using tex
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "econet.tex" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'econet.tex' failed with diagnostics:
running 'texi2dvi' on 'econet.tex' failed

LaTeX errors:
! LaTeX Error: File `orcidlink.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)


--- failed re-building 'econet.tex'

SUMMARY: processing the following file failed:
  'econet.tex'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'eggCountsExtra'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/eggCounts.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_eHDPrep.Rmd' using rmarkdown
! LaTeX Error: File `./images/Figure\unhbox \voidb@x \penalty \@M \hskip \z@ski
p \T1\textunderscore \discretionary {-}{}{}\penalty \@M \hskip \z@skip 1' not f
ound.

Error: processing vignette 'Introduction_to_eHDPrep.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/eHDPrep.Rcheck/vign_test/eHDPrep/vignettes/Introduction_to_eHDPrep.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Introduction_to_eHDPrep.log for more info.
--- failed re-building 'Introduction_to_eHDPrep.Rmd'

SUMMARY: processing the following file failed:
  'Introduction_to_eHDPrep.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  neighbours.h:17:12: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 14; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
  neighbours.h:20:12: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 14; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
  neighbours.h:39:12: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 14; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.1/enerscape.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.4Mb
Package suggested but not available for checking: 'epidict'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/escalation.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/eseis.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/espadon.Rcheck/00install.out' for details.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'EstimationTools-Ex.R' failed
The error most likely occurred in:

> ### Name: legend.HazardShape
> ### Title: Customize legend for 'plot.HazardShape' outputs
> ### Aliases: legend.HazardShape
> 
> ### ** Examples
> 
> library(EstimationTools)
> 
> data("reduction_cells")
> TTT_IG <- TTTE_Analytical(Surv(days, status) ~ 1, data = reduction_cells,
+                           method = 'censored')
> HS_IG <- TTT_hazard_shape(TTT_IG, data = reduction_cells)
> 
> #----------------------------------------------------------------------------
> # Example 1: put legend to the TTT plot of the reduction cells data set.
> 
> # Run `plot.HazardShape` method.
> par(
+   cex.lab=1.8,
+   cex.axis=1.8,
+   mar=c(4.8,5.4,1,1),
+   las = 1,
+   mgp=c(3.4,1,0)
+ )
> plot(HS_IG, pch = 16, cex = 1.8)
> 
> # Finally, put the legend
> legend.HazardShape(
+   x = "bottomright",
+   box.lwd = NA,
+   cex = 1.8,
+   pt.cex = 1.8,
+   bty = 'n',
+   pch = c(16, NA)
+ )
Error in legend(x, y, legend, fill, col, border, lty, lwd, pch, angle,  : 
  unused arguments (title.font, seg.len)
Calls: legend.HazardShape
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    extdata   4.0Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Packages required and available but unsuitable versions: 'grid', 'splines'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Found the following significant warnings:
  Warning: replacing previous import 'geiger::rescale' by 'phytools::rescale' when loading 'evobiR'
See 'd:/Rcompile/CRANpkg/local/4.1/evobiR.Rcheck/00install.out' for details.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: 'ExactData'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/expDB.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/extremis.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'exuberdata'
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
File 'fame/R/windows/zzz.R':
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section 'Good practice' in '?.onAttach'.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'FAMoS-EvaluationFunctions.Rmd' using rmarkdown
Error: processing vignette 'FAMoS-EvaluationFunctions.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'FAMoS-EvaluationFunctions.Rmd'

--- re-building 'FAMoS-Examples.Rmd' using rmarkdown
Error: processing vignette 'FAMoS-Examples.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'FAMoS-Examples.Rmd'

SUMMARY: processing the following files failed:
  'FAMoS-EvaluationFunctions.Rmd' 'FAMoS-Examples.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.5Mb
Package suggested but not available for checking: 'coxKM'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    Rcgi      2.8Mb
    cgi-bin   2.7Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'fastverse_intro.Rmd' using rmarkdown
Quitting from lines 104-108 (fastverse_intro.Rmd) 
Error: processing vignette 'fastverse_intro.Rmd' failed with diagnostics:
package or namespace load failed for 'fastverse':
 .onAttach failed in attachNamespace() for 'fastverse', details:
  call: NULL
  error: package or namespace load failed for 'magrittr':
 .onLoad failed in loadNamespace() for 'magrittr', details:
  call: fun(libname, pkgname)
  error: object 'magrittr_init' not found
--- failed re-building 'fastverse_intro.Rmd'

SUMMARY: processing the following file failed:
  'fastverse_intro.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.9Mb
Unexported objects imported by ':::' calls:
  'fdapace:::GCVLwls1D1' 'fdapace:::GetSmoothedMeanCurve'
  'fdapace:::HandleNumericsAndNAN' 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/fdaPDE.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.1/FGSG.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      2.2Mb
Package suggested but not available for checking: 'MicrobeDS'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       1.9Mb
    extdata   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    lib    5.7Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    9.0Mb
    libs   2.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    1.3Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'run_tests.R' [7s]
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > library(testthat)
  > library(formatters)
  > 
  > test_check("formatters", reporter = "check")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 152 ]
  
  == Failed tests ================================================================
  -- Failure ('test-txt_wrap.R:164:3'): row label wrapping has identical indentation --
  `res_vec` not identical to `exp_vec`.
  1/7 mismatches
  x[3]: " -----------------------"
  y[3]: " "
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 152 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.6Mb
    libs   2.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   6.6Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: 'dggrids'
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.7Mb
    libs  20.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/fs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ftExtra.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'fuzzyRankTests/libs/i386/fuzzyRankTests.dll':
  Found non-API calls to R: 'signrank_free', 'wilcox_free'
File 'fuzzyRankTests/libs/x64/fuzzyRankTests.dll':
  Found non-API calls to R: 'signrank_free', 'wilcox_free'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'chart_themes.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'chart_themes.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
Quitting from lines 240-253 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open URL 'https://www.cbioportal.org/api/api-docs'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    bin   8.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
installed size is 47.3Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'gasper-Ex.R' failed
The error most likely occurred in:

> ### Name: download_graph
> ### Title: Download sparse matrix form the SuiteSparse Matrix Collection.
> ### Aliases: download_graph
> 
> ### ** Examples
> 
> matrixname <- "grid1"
> groupname <- "AG-Monien"
> download_graph(matrixname,groupname)
trying URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Warning in download.file(url, temp) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file(url, temp) : 
  cannot open URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Calls: download_graph -> download.file
Execution halted
Running examples in 'gasper-Ex.R' failed
The error most likely occurred in:

> ### Name: download_graph
> ### Title: Download sparse matrix form the SuiteSparse Matrix Collection.
> ### Aliases: download_graph
> 
> ### ** Examples
> 
> matrixname <- "grid1"
> groupname <- "AG-Monien"
> download_graph(matrixname,groupname)
trying URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Warning in download.file(url, temp) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file(url, temp) : 
  cannot open URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Calls: download_graph -> download.file
Execution halted
Error(s) in re-building vignettes:
--- re-building 'gasper_vignette.rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
trying URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
Quitting from lines 52-56 (gasper_vignette.rmd) 
Error: processing vignette 'gasper_vignette.rmd' failed with diagnostics:
cannot open URL 'https://sparse.tamu.edu/MM/AG-Monien/grid1.tar.gz'
--- failed re-building 'gasper_vignette.rmd'

SUMMARY: processing the following file failed:
  'gasper_vignette.rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/gastempt.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gbfs)
  > 
  > test_check("gbfs")
  Initiating curl with CURL_SSL_BACKEND: openssl
  [ FAIL 1 | WARN 1 | SKIP 6 | PASS 10 ]
  
  == Skipped tests ===============================================================
  * On CRAN (5)
  * row-binding trips up on GHA (1)
  
  == Failed tests ================================================================
  -- Error ('test-wrapper.R:7:1'): (code run outside of `test_that()`) -----------
  Error in `value[[3L]](cond)`: There was an issue connecting with the given gbfs provider. The response is printed below: 
  Error in open.connection(con, "rb"): cannot open the connection
  
  Backtrace:
      x
   1. \-gbfs::get_gbfs("biketown_pdx") at test-wrapper.R:7:0
   2.   \-gbfs::get_which_gbfs_feeds(city = url)
   3.     \-base::tryCatch(jsonlite::fromJSON(txt = url), error = report_connection_issue)
   4.       \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.         \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.           \-value[[3L]](cond)
  
  [ FAIL 1 | WARN 1 | SKIP 6 | PASS 10 ]
  Error: Test failures
  Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/gbp.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 112.3Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     2.2Mb
    libs    98.1Mb
    proj     8.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   3.0Mb
    libs      2.8Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ###   Decimal degrees.
> ### Aliases: sexagesimal
> 
> ### ** Examples
> 
> # Latitude
> g <- -33
> m <- 38
> s <- 30.123456
> value <- sexagesimal(g, m, s, digits = 4)
> print(value)
[1] -33.6417
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  22.29 0.79 23.31 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'geomarocdata'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/geostan.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Packages required and available but unsuitable versions:
  'biomaRt', 'grDevices', 'graphics', 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'getwiki-Ex.R' failed
The error most likely occurred in:

> ### Name: get_wiki
> ### Title: Get the Text of a Wikipedia Article
> ### Aliases: get_wiki
> 
> ### ** Examples
> 
> get_wiki("United States")
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: get_wiki ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...s ,C_k)^\top = \mathbf {0}\,\,\text 
                                                  {and}\,\,\mathcal H_0: \ma...
l.236 ...H} (B_1,\ldots,B_k)^\top = \mathbf{0},}{}
                                                  
! Undefined control sequence.
<argument> ...\mathbf {C} = \mathbf {0}\,\, \text 
                                                  {or}\,\,\mathcal H_{0,\ell...
l.247 ...{B} = \mathbf{0}, \,\,\ell=1,\ldots,q,}{}
                                                  
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.249 ...s \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.250 \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                             , respectively, are calculated.
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.263 ...r \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.264 for \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                                 , the test statistics and c...
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       5.2Mb
    extdata   1.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'ggESDA-Ex.R' failed
The error most likely occurred in:

> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ggESDA.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building 'ggESDA.Rmd'

SUMMARY: processing the following file failed:
  'ggESDA.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ggip.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ggiraph.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggOceanMapsData'
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   1.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ggraph.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    1.8Mb
    libs   2.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/gllvm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs            8.5Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Error(s) in re-building vignettes:
--- re-building 'intro.rmd' using rmarkdown
trying URL 'https://web.stanford.edu/~hastie/glmnet/glmnetData/Leukemia.RData'
Quitting from lines 167-173 (intro.rmd) 
Error: processing vignette 'intro.rmd' failed with diagnostics:
cannot open URL 'https://web.stanford.edu/~hastie/glmnet/glmnetData/Leukemia.RData'
--- failed re-building 'intro.rmd'

SUMMARY: processing the following file failed:
  'intro.rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'glmtlp.Rmd' using rmarkdown
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

Error: processing vignette 'glmtlp.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/glmtlp.Rcheck/vign_test/glmtlp/vignettes/glmtlp.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See glmtlp.log for more info.
--- failed re-building 'glmtlp.Rmd'

SUMMARY: processing the following file failed:
  'glmtlp.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/glossr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R   6.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(grafzahl)
  > 
  > test_check("grafzahl")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  
  == Failed tests ================================================================
  -- Failure ('test_grafzahl.R:10:5'): basic -------------------------------------
  `grafzahl(...)` threw an unexpected error.
  Message: Fail to download the model `bert-base-cased` from Hugging Face
  Class:   simpleError/error/condition
  Backtrace:
       x
    1. +-testthat::expect_error(...) at test_grafzahl.R:10:4
    2. | \-testthat:::expect_condition_matching(...)
    3. |   \-testthat:::quasi_capture(...)
    4. |     +-testthat (local) .capture(...)
    5. |     | \-base::withCallingHandlers(...)
    6. |     \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. +-grafzahl::grafzahl(...)
    8. \-grafzahl:::grafzahl.character(...)
    9.   +-grafzahl::grafzahl(...)
   10.   \-grafzahl:::grafzahl.corpus(...)
   11.     \-grafzahl:::.check_model_type(model_type = model_type, model_name = model_name)
   12.       \-grafzahl:::.infer_model_type(model_name)
   13.         \-grafzahl:::.download_from_huggingface(model_name)
   14.           \-base::tryCatch(...)
   15.             \-base (local) tryCatchList(expr, classes, parentenv, handlers)
   16.               \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17.                 \-value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'graticule-Ex.R' failed
The error most likely occurred in:

> ### Name: lonlat
> ### Title: Add longitude latitude lines to a plot
> ### Aliases: lonlat
> 
> ### ** Examples
> 
> plot(c(-180, 180), c(-90, 90))
> lonlat(raster::raster())
> 
> p <- raster::projectExtent(raster::raster(), "+proj=igh")
> lonlat(p, add = FALSE)
Error in proj4::ptransform(x, source, target, ...) : 
  major axis or radius = 0 or not given
Calls: lonlat
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    2.7Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Package required and available but unsuitable version: 'fs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: unable to re-encode 'guiplotServer.R' line 852
See 'd:/Rcompile/CRANpkg/local/4.1/guiplot.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 182.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  179.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs    2.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   3.9Mb
    doc     4.0Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  
  == Failed tests ================================================================
  -- Failure ('testall.R:22:3'): test the haze -----------------------------------
  floor(h$haze * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 225, 224).
  1/1 mismatches
  [1] 224 - 225 == -1
  -- Failure ('testall.R:23:3'): test the haze -----------------------------------
  floor(h$A0 * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 710, 712).
  1/1 mismatches
  [1] 712 - 710 == 2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/hbamr.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'hedgehog.Rmd' using rmarkdown
Error: processing vignette 'hedgehog.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'hedgehog.Rmd'

--- re-building 'state-machines.Rmd' using rmarkdown
Error: processing vignette 'state-machines.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'state-machines.Rmd'

SUMMARY: processing the following files failed:
  'hedgehog.Rmd' 'state-machines.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/hellorust.Rcheck/00install.out' for details.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.6Mb
    libs   2.2Mb
GNU make is a SystemRequirements.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
':::' call which should be '::': 'ggplot2:::guide_axis'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/highs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/historicalborrowlong.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.6Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
NB: this package is only installed for sub-architecture 'x64'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Package suggested but not available for checking: 'ROI.plugin.mosek'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.5Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/hsstan.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Running examples in 'htm2txt-Ex.R' failed
The error most likely occurred in:

> ### Name: browse
> ### Title: Display simple plain texts in a web page at a certain URL
> ### Aliases: browse
> 
> ### ** Examples
> 
> browse("https://www.wikipedia.org/")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: browse ... htm2txt -> as.vector -> unlist -> paste -> readLines -> file
Execution halted
Running examples in 'htmcglm-Ex.R' failed
The error most likely occurred in:

> ### Name: mc_anova_I
> ### Title: ANOVA type I table for mcglm objects via Wald test.
> ### Aliases: mc_anova_I
> 
> ### ** Examples
> 
> 
> library(mcglm)
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    http://mcglm.leg.ufpr.br/

  mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
----------------------------------------------------------------------
> library(Matrix)
> library(htmcglm)
> 
> data("soya", package = "mcglm")
> 
> form.grain <- grain ~ water * pot
> form.seed <- seeds ~ water * pot
> 
> soya$viablepeasP <- soya$viablepeas / soya$totalpeas
> form.peas <- viablepeasP ~ water * pot
> 
> Z0 <- mc_id(soya)
> Z1 <- mc_mixed(~0 + factor(block), data = soya)
> 
> fit_joint <- mcglm(linear_pred = c(form.grain,
+                                    form.seed,
+                                    form.peas),
+                    matrix_pred = list(c(Z0, Z1),
+                                       c(Z0, Z1),
+                                       c(Z0, Z1)),
+                    link = c("identity",
+                             "log",
+                             "logit"),
+                    variance = c("constant",
+                                 "tweedie",
+                                 "binomialP"),
+                    Ntrial = list(NULL,
+                                  NULL,
+                                  soya$totalpeas),
+                    power_fixed = c(TRUE,TRUE,TRUE),
+                    data = soya)
Automatic initial values selected. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
Error: $ operator is invalid for atomic vectors
Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'design-principles.Rmd' using rmarkdown
--- finished re-building 'design-principles.Rmd'

--- re-building 'huxreg.Rmd' using rmarkdown
--- finished re-building 'huxreg.Rmd'

--- re-building 'huxtable.Rmd' using rmarkdown
! Missing \endcsname inserted.
<to be read again> 
                   \egroup 
l.148 \begin
            {threeparttable} 

Error: processing vignette 'huxtable.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/huxtable.Rcheck/vign_test/huxtable/vignettes/huxtable.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See huxtable.log for more info.
--- failed re-building 'huxtable.Rmd'

--- re-building 'themes.Rhtml' using knitr
--- finished re-building 'themes.Rhtml'

SUMMARY: processing the following file failed:
  'huxtable.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'hyd1d-Ex.R' failed
The error most likely occurred in:

> ### Name: getPegelonlineW
> ### Title: Get W from pegelonline.wsv.de for the specified gauging station
> ###   and time
> ### Aliases: getPegelonlineW
> 
> ### ** Examples
> 
> getPegelonlineW(gauging_station = "DESSAU", time = Sys.time() - 3600)
Warning in utils::download.file(url, tf, method = method, quiet = TRUE) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in value[[3L]](cond) : 
  It was not possible to access gauging data from
https://pegelonline.wsv.de
Please try again later.
Error in utils::download.file(url, tf, method = method, quiet = TRUE): cannot open URL 'https://www.pegelonline.wsv.de/webservices/rest-api/v2/stations/1edc5fa4-88af-47f5-95a4-0e77a06fe8b1/W/measurements.json?start=2023-04-04T00:00%2B01:00&end=2023-04-04T12:59%2B01:00'
Calls: getPegelonlineW ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'hyd1d.Rmd' using rmarkdown
Quitting from lines 361-391 (hyd1d.Rmd) 
Error: processing vignette 'hyd1d.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building 'hyd1d.Rmd'

--- re-building 'vignette_DE.Rmd' using rmarkdown
Quitting from lines 1166-1191 (vignette_DE.Rmd) 
Error: processing vignette 'vignette_DE.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building 'vignette_DE.Rmd'

SUMMARY: processing the following files failed:
  'hyd1d.Rmd' 'vignette_DE.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'DecisionNetworks.Rmd' using rmarkdown
--- finished re-building 'DecisionNetworks.Rmd'

--- re-building 'GettingStartedWithHydeNet.Rmd' using rmarkdown
--- finished re-building 'GettingStartedWithHydeNet.Rmd'

--- re-building 'HydeNetPlots.Rmd' using rmarkdown
Quitting from lines 158-167 (HydeNetPlots.Rmd) 
Error: processing vignette 'HydeNetPlots.Rmd' failed with diagnostics:
Graphviz link does not exist. Find a new link
--- failed re-building 'HydeNetPlots.Rmd'

--- re-building 'WorkingWithHydeNetObjects.Rmd' using rmarkdown
--- finished re-building 'WorkingWithHydeNetObjects.Rmd'

SUMMARY: processing the following file failed:
  'HydeNetPlots.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
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    extdata   5.5Mb
    libs      2.2Mb
installed size is  5.2Mb
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    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/IFAA.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
> model$output$fit
[1] 0.4515827
> model$output$gradient
x1 
 0 
> model$output$hessian
   x1
x1  8
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.71 0.53 8.27 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Package suggested but not available for checking: 'IFCdata'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.4Mb
    libs  13.4Mb
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.7Mb
installed size is 12.6Mb
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    dlib-19.20   9.1Mb
    libs         2.8Mb
installed size is  7.0Mb
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    libs   6.8Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     16.0Mb
installed size is 30.5Mb
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    libs   19.3Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
    libs   2.0Mb
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:

> ### Name: repLoad
> ### Title: Load immune repertoire files into the R workspace
> ### Aliases: repLoad
> 
> ### ** Examples
> 
> # To load the data from a single file (note that you don't need to specify the data format):
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/Sample1.tsv.gz")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Processing "<initial>" ...
  -- [1/1] Parsing "D:/temp/RtmpUnBNXd/RLIBS_22787de72ee6/immunarch/extdata/io/Sample1.tsv.gz" -- immunarch

== Step 2/3: checking metadata files and merging files... ==

Processing "<initial>" ...
  -- Metadata file not found; creating a dummy metadata...

== Step 3/3: processing paired chain data... ==

Done!

> 
> # Suppose you have a following structure in your folder:
> # >_ ls
> # immunoseq1.txt
> # immunoseq2.txt
> # immunoseq3.txt
> # metadata.txt
> 
> # To load the whole folder with every file in it type:
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Error in .split_to_batches(.path, "<initial>") : 
  Input file or directory not found: D:/temp/RtmpUnBNXd/RLIBS_22787de72ee6/immunarch/extdata/io/
Calls: repLoad -> .split_to_batches
Execution halted
Running examples in 'immunarch-Ex.R' failed
The error most likely occurred in:

> ### Name: repLoad
> ### Title: Load immune repertoire files into the R workspace
> ### Aliases: repLoad
> 
> ### ** Examples
> 
> # To load the data from a single file (note that you don't need to specify the data format):
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/Sample1.tsv.gz")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Processing "<initial>" ...
  -- [1/1] Parsing "D:/temp/RtmpUnBNXd/RLIBS_22787de72ee6/immunarch/extdata/io/Sample1.tsv.gz" -- immunarch

== Step 2/3: checking metadata files and merging files... ==

Processing "<initial>" ...
  -- Metadata file not found; creating a dummy metadata...

== Step 3/3: processing paired chain data... ==

Done!

> 
> # Suppose you have a following structure in your folder:
> # >_ ls
> # immunoseq1.txt
> # immunoseq2.txt
> # immunoseq3.txt
> # metadata.txt
> 
> # To load the whole folder with every file in it type:
> file_path <- paste0(system.file(package = "immunarch"), "/extdata/io/")
> immdata <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Error in .split_to_batches(.path, "<initial>") : 
  Input file or directory not found: D:/temp/RtmpUnBNXd/RLIBS_22787de72ee6/immunarch/extdata/io/
Calls: repLoad -> .split_to_batches
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.1Mb
    libs   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
GNU make is a SystemRequirements.
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/intervals.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'irace-package.Rnw' using knitr
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "irace-package.tex" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'irace-package.Rnw' failed with diagnostics:
running 'texi2dvi' on 'irace-package.tex' failed

LaTeX errors:
age.tex:1021: Package enumitem Error: left undefined.

See the enumitem package documentation for explanation.
Type  H <return>  for immediate help
Try typing  <return>  to proceed.

--- failed re-building 'irace-package.Rnw'

SUMMARY: processing the following file failed:
  'irace-package.Rnw'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    doc   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Running examples in 'IsoMemo-Ex.R' failed
The error most likely occurred in:

> ### Name: getData
> ### Title: API wrapper that fetches data from IsoMemo Applications
> ### Aliases: getData
> 
> ### ** Examples
> 
> getData(db = "IntChron")
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: getData ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IsoMemo)
  > 
  > test_check("IsoMemo")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  == Failed tests ================================================================
  -- Error ('test-01-getData.R:2:3'): getData() actually retrieves all data ------
  Error in `open.connection(con, "rb")`: cannot open the connection
  Backtrace:
      x
   1. \-IsoMemo::getData() at test-01-getData.R:2:2
   2.   \-IsoMemo::getDatabaseList()
   3.     \-IsoMemo:::callAPI("dbsources")
   4.       \-jsonlite::fromJSON(url)
   5.         \-jsonlite:::parse_and_simplify(...)
   6.           \-jsonlite:::parseJSON(txt, bigint_as_char)
   7.             \-jsonlite:::parse_con(txt, bigint_as_char)
   8.               +-base::open(con, "rb")
   9.               \-base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Using-IsoMemo-API.Rmd' using rmarkdown
Quitting from lines 21-23 (Using-IsoMemo-API.Rmd) 
Error: processing vignette 'Using-IsoMemo-API.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'Using-IsoMemo-API.Rmd'

SUMMARY: processing the following file failed:
  'Using-IsoMemo-API.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.2Mb
    data   1.5Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           9.1Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    docs   3.5Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'janitor.Rmd' using rmarkdown
pandoc.exe: Unknown extension: gfm_auto_identifiers
Error: processing vignette 'janitor.Rmd' failed with diagnostics:
pandoc document conversion failed with error 7
--- failed re-building 'janitor.Rmd'

--- re-building 'tabyls.Rmd' using rmarkdown
Error: processing vignette 'tabyls.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'tabyls.Rmd'

SUMMARY: processing the following files failed:
  'janitor.Rmd' 'tabyls.Rmd'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'audit-sampling.Rmd' using rmarkdown
--- finished re-building 'audit-sampling.Rmd'

--- re-building 'bayesian-sampling-workflow.Rmd' using rmarkdown
--- finished re-building 'bayesian-sampling-workflow.Rmd'

--- re-building 'creating-prior.Rmd' using rmarkdown
--- finished re-building 'creating-prior.Rmd'

--- re-building 'data-auditing.Rmd' using rmarkdown
--- finished re-building 'data-auditing.Rmd'

--- re-building 'digit-analysis.Rmd' using rmarkdown
--- finished re-building 'digit-analysis.Rmd'

--- re-building 'jfa.Rmd' using rmarkdown
--- finished re-building 'jfa.Rmd'

--- re-building 'sample-evaluation.Rmd' using rmarkdown
--- finished re-building 'sample-evaluation.Rmd'

--- re-building 'sample-planning.Rmd' using rmarkdown
--- finished re-building 'sample-planning.Rmd'

--- re-building 'sample-selection.Rmd' using rmarkdown
--- finished re-building 'sample-selection.Rmd'

--- re-building 'sampling-workflow.Rmd' using rmarkdown
Error: processing vignette 'sampling-workflow.Rmd' failed with diagnostics:
pandoc document conversion failed with error 5
--- failed re-building 'sampling-workflow.Rmd'

SUMMARY: processing the following file failed:
  'sampling-workflow.Rmd'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'JFE-Ex.R' failed
The error most likely occurred in:

> ### Name: getFed
> ### Title: Download financial and economic time series data from the Fed
> ### Aliases: getFed
> 
> ### ** Examples
> 
> 
> getFed(var.name="UNRATE")$data
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(file, "rt") : cannot open the connection
Calls: getFed -> read.csv -> read.table -> file
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/latticeExtra.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'lazyNumbers-Ex.R' failed
The error most likely occurred in:

> ### Name: lazyVector
> ### Title: Lazy vector
> ### Aliases: lazyVector as.lazyVector as.lazyNumber lazyvec lazynb
> 
> ### ** Examples
> 
> library(lazyNumbers)
> x <- lazynb(1) - lazynb(7) * lazynb(0.1)
> as.double(x)
[1] 0.3
> # shorter:
> x <- 1 - lazynb(7) * 0.1
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.31 0.03 1.34 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ldt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  11.0Mb
Package suggested but not available for checking: 'doMC'
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'less-Ex.R' failed
The error most likely occurred in:

> ### Name: test_timing
> ### Title: Compare Fitting Time
> ### Aliases: test_timing
> 
> ### ** Examples
> 
> X <- matrix(sample(100, 20), nrow = 10)
> y <- sample(100, 10)
> test_timing(1, X, y)
Error in barplot.default(unlist(timings), main = "Fitting Time of Different Regressors",  : 
  log scale error: at least one 'height + offset' value <= 0
Calls: test_timing -> barplot -> barplot.default
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/lfe.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'doMC'
Initiating curl with CURL_SSL_BACKEND: openssl
Package unavailable to check Rd xrefs: 'doMC'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Initiating curl with CURL_SSL_BACKEND: openssl
Package unavailable to check Rd xrefs: 'rsyslog'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/lidR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   2.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [54s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lime)
  > 
  > test_check("lime")
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 22 ]
  
  == Skipped tests ===============================================================
  * On CRAN (1)
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 22 ]
  > 
  > proc.time()
     user  system elapsed 
    52.68    0.57   53.60
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Codoc mismatches from documentation object 'gloss_example':
gloss_example
  Code: function(transliteration, glosses, free_translation = "",
                 comment = "", annotation = NULL, grammaticality =
                 NULL, audio_path = NULL, audio_label = "<U+266A>",
                 video_path = NULL, video_width = 320, video_height =
                 240, line_length = 70, italic_transliteration =
                 getOption("lingglosses.italic_transliteration"),
                 drop_transliteration = FALSE, intext = FALSE,
                 write_to_db = TRUE)
  Docs: function(transliteration, glosses, free_translation = "",
                 comment = "", annotation = NULL, grammaticality =
                 NULL, audio_path = NULL, audio_label = "<U+266A>",
                 video_path = NULL, video_width = 320, video_height =
                 240, line_length = 70, italic_transliteration =
                 getOption("lingglosses.italic_transliteration"),
                 drop_transliteration = FALSE, intext = FALSE,
                 write_to_db = TRUE)
  Mismatches in argument default values:
    Name: 'audio_label' Code: "<U+266A>" Docs: "<U+266A>"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       2.6Mb
    testdata   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/LMMELSM.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
Initiating curl with CURL_SSL_BACKEND: openssl
Package unavailable to check Rd xrefs: 'rsyslog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs   2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  liblwgeom/lwgeom_topo.c:4305:36: warning: too many arguments for format [-Wformat-extra-args]
  liblwgeom/lwgeom_topo.c:4357:38: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.1/lwgeom.Rcheck/00install.out' for details.
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(madrat)
  Loading required package: magclass
  > 
  > test_check("madrat")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  
  == Skipped tests ===============================================================
  * On CRAN (6)
  * reshape2 cannot be loaded (1)
  
  == Failed tests ================================================================
  -- Failure ('test-config.R:3:3'): cache folder can be set properly -------------
  getwd() not identical to getConfig("cachefolder").
  1/1 mismatches
  x[1]: "d:/Rcompile/CRANpkg/local/4.1/madrat.Rcheck/tests/testthat"
  y[1]: "d:/RCompile/CRANpkg/local/4.1/madrat.Rcheck/tests/testthat"
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is 77.3Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  70.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mapdeck.Rcheck/00install.out' for details.
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'flashier'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'gurobi'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
Package required but not available: 'rolog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  validity.c:100:18: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.1/Matrix.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   3.0Mb
Running examples in 'mcglm-Ex.R' failed
The error most likely occurred in:

> ### Name: Hunting
> ### Title: Hunting in Pico Basile, Bioko Island, Equatorial Guinea.
> ### Aliases: Hunting
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(mcglm)
> library(Matrix)
> data(Hunting, package="mcglm")
> formu <- OT ~ METHOD*ALT + SEX + ALT*poly(MONTH, 4)
> Z0 <- mc_id(Hunting)
> Z1 <- mc_mixed(~0 + HUNTER.MONTH, data = Hunting)
> fit <- mcglm(linear_pred = c(formu), matrix_pred = list(c(Z0, Z1)),
+             link = c("log"), variance = c("poisson_tweedie"),
+             power_fixed = c(FALSE),
+             control_algorithm = list(max_iter = 100),
+             offset = list(log(Hunting$OFFSET)), data = Hunting)
Automatic initial values selected. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
Error: $ operator is invalid for atomic vectors
Execution halted
Running examples in 'mcglm-Ex.R' failed
The error most likely occurred in:

> ### Name: Hunting
> ### Title: Hunting in Pico Basile, Bioko Island, Equatorial Guinea.
> ### Aliases: Hunting
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(mcglm)
> library(Matrix)
> data(Hunting, package="mcglm")
> formu <- OT ~ METHOD*ALT + SEX + ALT*poly(MONTH, 4)
> Z0 <- mc_id(Hunting)
> Z1 <- mc_mixed(~0 + HUNTER.MONTH, data = Hunting)
> fit <- mcglm(linear_pred = c(formu), matrix_pred = list(c(Z0, Z1)),
+             link = c("log"), variance = c("poisson_tweedie"),
+             power_fixed = c(FALSE),
+             control_algorithm = list(max_iter = 100),
+             offset = list(log(Hunting$OFFSET)), data = Hunting)
Automatic initial values selected. 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
Error: $ operator is invalid for atomic vectors
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GLMExamples.Rmd' using rmarkdown
Loading required package: mcglm
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    http://mcglm.leg.ufpr.br/

  mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
----------------------------------------------------------------------
Loading required package: Matrix
Quitting from lines 67-77 (GLMExamples.Rmd) 
Error: processing vignette 'GLMExamples.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'GLMExamples.Rmd'

--- re-building 'UniModels.Rmd' using rmarkdown
Loading required package: mcglm
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    http://mcglm.leg.ufpr.br/

  mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
----------------------------------------------------------------------
Loading required package: Matrix
Loading required package: mvtnorm
Loading required package: tweedie
Quitting from lines 52-80 (UniModels.Rmd) 
Error: processing vignette 'UniModels.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'UniModels.Rmd'

SUMMARY: processing the following files failed:
  'GLMExamples.Rmd' 'UniModels.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [97s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("mcmcsae")
  Loading required package: mcmcsae
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 383 ]
  
  == Failed tests ================================================================
  -- Failure ('test_linreg.R:35:3'): single-site Gibbs sampler works -------------
  (0.5 < summ$mu[, "Mean"]) && (summ$mu[, "Mean"] < 2) is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  -- Failure ('test_linreg.R:36:3'): single-site Gibbs sampler works -------------
  (0.5 < summ$beta1[, "Mean"]) && (summ$beta1[, "Mean"] < 2) is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  -- Failure ('test_linreg.R:37:3'): single-site Gibbs sampler works -------------
  (2 * 0.5 < summ$beta2[, "Mean"]) && (summ$beta2[, "Mean"] < 2 * 
      2) is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  -- Failure ('test_linreg.R:38:3'): single-site Gibbs sampler works -------------
  (3 * 0.5 < summ$beta3[, "Mean"]) && (summ$beta3[, "Mean"] < 3 * 
      2) is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  -- Failure ('test_linreg.R:39:3'): single-site Gibbs sampler works -------------
  (4 * 0.5 < summ$beta4[, "Mean"]) && (summ$beta4[, "Mean"] < 4 * 
      2) is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  -- Failure ('test_linreg.R:40:3'): single-site Gibbs sampler works -------------
  (0.5 < summ$sigma_[, "Mean"]) && (summ$sigma_[, "Mean"] < 2) is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 383 ]
  Error: Test failures
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/MeshesTools.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'genuMet'
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'metacoder-Ex.R' failed
The error most likely occurred in:

> ### Name: arrange_obs
> ### Title: Sort user data in [taxmap()] objects
> ### Aliases: arrange_obs
> 
> ### ** Examples
> 
> # Sort in ascending order
> arrange_obs(ex_taxmap, "info", n_legs)
<Taxmap>
  17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
  17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
  4 data sets:
    info:
Error:
! The `n_extra` argument of `print()` was deprecated in pillar 1.6.2 and
  is now defunct.
i Please use the `max_extra_cols` argument instead.
Backtrace:
     x
  1. +-base (local) `<fn>`(x)
  2. \-R6:::print.R6(x)
  3.   \-.subset2(x, "print")(...)
  4.     \-metacoder:::print_item(...) at metacoder/R/old_taxa--taxmap--class.R:97:10
  5.       \-get(best_method)(...)
  6.         +-base::paste0(...)
  7.         +-utils::capture.output(...)
  8.         | \-base::withVisible(...elt(i))
  9.         +-base::print(...)
 10.         \-pillar:::print.tbl(...)
 11.           \-pillar:::print_tbl(...)
 12.             \-lifecycle::deprecate_stop(...)
 13.               \-lifecycle:::deprecate_stop0(msg)
 14.                 \-rlang::cnd_signal(...)
Execution halted
Running examples in 'metacoder-Ex.R' failed
The error most likely occurred in:

> ### Name: arrange_obs
> ### Title: Sort user data in [taxmap()] objects
> ### Aliases: arrange_obs
> 
> ### ** Examples
> 
> # Sort in ascending order
> arrange_obs(ex_taxmap, "info", n_legs)
<Taxmap>
  17 taxa: b. Mammalia, c. Plantae ... q. lycopersicum, r. tuberosum
  17 edges: NA->b, NA->c, b->d, b->e ... j->o, k->p, l->q, l->r
  4 data sets:
    info:
Error:
! The `n_extra` argument of `print()` was deprecated in pillar 1.6.2 and
  is now defunct.
i Please use the `max_extra_cols` argument instead.
Backtrace:
     x
  1. +-base (local) `<fn>`(x)
  2. \-R6:::print.R6(x)
  3.   \-.subset2(x, "print")(...)
  4.     \-metacoder:::print_item(...) at metacoder/R/old_taxa--taxmap--class.R:97:10
  5.       \-get(best_method)(...)
  6.         +-base::paste0(...)
  7.         +-utils::capture.output(...)
  8.         | \-base::withVisible(...elt(i))
  9.         +-base::print(...)
 10.         \-pillar:::print.tbl(...)
 11.           \-pillar:::print_tbl(...)
 12.             \-lifecycle::deprecate_stop(...)
 13.               \-lifecycle:::deprecate_stop0(msg)
 14.                 \-rlang::cnd_signal(...)
Execution halted
Running 'testthat.R' [65s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  [ FAIL 1 | WARN 2 | SKIP 3 | PASS 524 ]
  
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  == Failed tests ================================================================
  -- Error ('test--taxmap.R:214:3'): Print methods works -------------------------
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `n_extra` argument of `print()` was deprecated in pillar 1.6.2 and
  is now defunct.
  i Please use the `max_extra_cols` argument instead.
  Backtrace:
       x
    1. +-testthat::expect_output(print(x), "<Taxmap>.+17 taxa.+17 edges.+1 functions.+reaction") at test--taxmap.R:214:2
    2. | \-testthat:::quasi_capture(...)
    3. |   +-testthat (local) .capture(...)
    4. |   | \-testthat::capture_output_lines(code, print, width = width)
    5. |   |   \-testthat:::eval_with_output(code, print = print, width = width)
    6. |   |     +-withr::with_output_sink(path, withVisible(code))
    7. |   |     | \-base::force(code)
    8. |   |     \-base::withVisible(code)
    9. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. +-base::print(x)
   11. \-R6:::print.R6(x)
   12.   \-.subset2(x, "print")(...)
   13.     \-metacoder:::print_item(...)
   14.       \-get(best_method)(...)
   15.         +-base::paste0(...)
   16.         +-utils::capture.output(...)
   17.         | \-base::withVisible(...elt(i))
   18.         +-base::print(...)
   19.         \-pillar:::print.tbl(...)
   20.           \-pillar:::print_tbl(...)
   21.             \-lifecycle::deprecate_stop(...)
   22.               \-lifecycle:::deprecate_stop0(msg)
   23.                 \-rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 2 | SKIP 3 | PASS 524 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [66s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  [ FAIL 1 | WARN 2 | SKIP 3 | PASS 524 ]
  
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  == Failed tests ================================================================
  -- Error ('test--taxmap.R:214:3'): Print methods works -------------------------
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `n_extra` argument of `print()` was deprecated in pillar 1.6.2 and
  is now defunct.
  i Please use the `max_extra_cols` argument instead.
  Backtrace:
       x
    1. +-testthat::expect_output(print(x), "<Taxmap>.+17 taxa.+17 edges.+1 functions.+reaction") at test--taxmap.R:214:2
    2. | \-testthat:::quasi_capture(...)
    3. |   +-testthat (local) .capture(...)
    4. |   | \-testthat::capture_output_lines(code, print, width = width)
    5. |   |   \-testthat:::eval_with_output(code, print = print, width = width)
    6. |   |     +-withr::with_output_sink(path, withVisible(code))
    7. |   |     | \-base::force(code)
    8. |   |     \-base::withVisible(code)
    9. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. +-base::print(x)
   11. \-R6:::print.R6(x)
   12.   \-.subset2(x, "print")(...)
   13.     \-metacoder:::print_item(...)
   14.       \-get(best_method)(...)
   15.         +-base::paste0(...)
   16.         +-utils::capture.output(...)
   17.         | \-base::withVisible(...elt(i))
   18.         +-base::print(...)
   19.         \-pillar:::print.tbl(...)
   20.           \-pillar:::print_tbl(...)
   21.             \-lifecycle::deprecate_stop(...)
   22.               \-lifecycle:::deprecate_stop0(msg)
   23.                 \-rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 2 | SKIP 3 | PASS 524 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/MetaStan.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   2.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.6Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'MFSIS-Ex.R' failed
The error most likely occurred in:

> ### Name: PCSIS
> ### Title: Model-Free Feature Screening Based on the Projection Correlation
> ### Aliases: PCSIS
> 
> ### ** Examples
> 
> 
> have_numpy=reticulate::py_module_available("numpy")
> if (have_numpy){
+ req_py()
+ library(MFSIS)
+ n=20;
+ p=50;
+ rho=0.5;
+ data=GendataLM(n,p,rho,error="gaussian")
+ data=cbind(data[[1]],data[[2]])
+ colnames(data)[1:ncol(data)]=c(paste0("X",1:(ncol(data)-1)),"Y")
+ data=as.matrix(data)
+ X=data[,1:(ncol(data)-1)];
+ Y=data[,ncol(data)];
+ A=PCSIS(X,Y,n/log(n));A
+ }else{
+    print('You should have the Python testing environment!')
+ }
vIt is detected that you have configured the necessary Python environmemt! 

vIt is detected that you have configured the necessary Python module! 

vIt is detected that you have configured the necessary Python environmemt! 

vIt is detected that you have configured the necessary Python module!
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.266 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   (\eqn{p > 1}{}) distribut...
! Undefined control sequence.
<recently read> \mathbb 
                        
l.268 ..., a random vector of \eqn{\mathbb{R}^p}{}
                                                   distributed according to ...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    lib    1.3Mb
    libs   2.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Running examples in 'MinkowskiSum-Ex.R' failed
The error most likely occurred in:

> ### Name: MinkowskiSum
> ### Title: Minkowski sum of two meshes
> ### Aliases: MinkowskiSum
> 
> ### ** Examples
> 
> # example 1: octahedron + icosahedron
> library(MinkowskiSum)
> library(rgl)
> mesh1 <- octahedron3d()
> mesh2 <- icosahedron3d()
> mesh <- MinkowskiSum(mesh1, mesh2, normals = FALSE)
â Processing mesh nÂ°1...
Successful polygon orientation.
The mesh is triangle.
The mesh is closed.
The mesh bounds a volume.
... done.

â Processing mesh nÂ°2...
Successful polygon orientation.
The mesh is triangle.
The mesh is closed.
The mesh bounds a volume.
... done.

> rglmesh <- toRGL(mesh)
> open3d(windowRect = c(50, 50, 562, 562))
wgl 
  1 
> view3d(30, 30, zoom = 0.8)
> shade3d(rglmesh, color = "maroon")
> plotEdges(mesh[["vertices"]], mesh[["edges0"]], color = "darkred")
> 
> # example2: truncated icosahedron + tetrahedron
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:rgl'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.43 0.16 2.72 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/MIRES.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'missForest_1.5.Rnw' using Sweave
Loading required package: foreach
Loading required package: missForest
Warning in file(file, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'

Error: processing vignette 'missForest_1.5.Rnw' failed with diagnostics:
 chunk 15 (label = muskData) 
Error in file(file, "r") : cannot open the connection

--- failed re-building 'missForest_1.5.Rnw'

SUMMARY: processing the following file failed:
  'missForest_1.5.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
Initiating curl with CURL_SSL_BACKEND: openssl
Found the following significant warnings:
  ./mlpack/core/data/save_impl.hpp:107:16: warning: 'bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = unsigned int; std::ostream = std::basic_ostream<char>]' is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:128:16: warning: 'bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = unsigned int; std::ostream = std::basic_ostream<char>]' is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:107:16: warning: 'bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long long unsigned int; std::ostream = std::basic_ostream<char>]' is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:128:16: warning: 'bool arma::Mat<eT>::quiet_save(std::ostream&, arma::file_type) const [with eT = long long unsigned int; std::ostream = std::basic_ostream<char>]' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.1/mlpack.Rcheck/00install.out' for details.
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'alstructure'

Package which this enhances but not available for checking: 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/moexer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.4Mb
Error(s) in re-building vignettes:
--- re-building 'dermatitis.Rmd' using rmarkdown
--- finished re-building 'dermatitis.Rmd'

--- re-building 'genetic_example.Rmd' using rmarkdown
Quitting from lines 60-61 (genetic_example.Rmd) 
Error: processing vignette 'genetic_example.Rmd' failed with diagnostics:
The `n_extra` argument of `print()` was deprecated in pillar 1.6.2 and
is now defunct.
i Please use the `max_extra_cols` argument instead.
--- failed re-building 'genetic_example.Rmd'

--- re-building 'outlier_intro.Rmd' using rmarkdown
--- finished re-building 'outlier_intro.Rmd'

SUMMARY: processing the following file failed:
  'genetic_example.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'moranajp-Ex.R' failed
The error most likely occurred in:

> ### Name: draw_bigram_network
> ### Title: Draw bigram network using morphological analysis data.
> ### Aliases: draw_bigram_network bigram bigram_depend bigram_network
> ###   word_freq bigram_network_plot
> 
> ### ** Examples
> 
> library(magrittr)
> data(synonym)
> synonym <- unescape_utf(synonym)
> 
> data(neko_mecab)
> neko_mecab <- 
+   neko_mecab  %>%
+   unescape_utf() %>%
+   add_sentence_no() %>%
+   clean_up(use_common_data = TRUE, synonym_df = synonym)
Joining with `by = join_by(`<U+539F><U+5F62>`)`
> 
> bigram_neko <- 
+   neko_mecab %>%
+   draw_bigram_network()
Warning in bigram(df, ...) :
  Not used group. sentence has only one category.
Error in UseMethod("slice") : 
  no applicable method for 'slice' applied to an object of class "character"
Calls: %>% ... draw_bigram_network -> bigram_network -> <Anonymous>
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/Morpho.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'MorphoTools2_tutorial.Rmd' using rmarkdown
! Paragraph ended before \@xverbatim was complete.
<to be read again> 
                   \par 
l.123 

Error: processing vignette 'MorphoTools2_tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/MorphoTools2.Rcheck/vign_test/MorphoTools2/vignettes/MorphoTools2_tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MorphoTools2_tutorial.log for more info.
--- failed re-building 'MorphoTools2_tutorial.Rmd'

SUMMARY: processing the following file failed:
  'MorphoTools2_tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs     2.3Mb
    raster   2.2Mb
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(motifr)
  > library(reticulate)
  > 
  > test_check("motifr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  
  == Failed tests ================================================================
  -- Error ('test-core.R:43:3'): io_undirected_dummy_net_issue#27 ----------------
  <Rcpp::exception/C++Error/error/condition>
  Error: TypeError: 'float' object cannot be interpreted as an integer
  
  Backtrace:
       x
    1. +-reticulate::py_suppress_warnings(motif_summary(ml_net27, lvl_attr = "lvl")) at test-core.R:43:2
    2. | +-base::with(warnings$catch_warnings(), expr)
    3. | \-reticulate:::with.python.builtin.object(...)
    4. |   +-base::tryCatch(...)
    5. |   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
    6. |   \-base::force(expr)
    7. \-motifr::motif_summary(ml_net27, lvl_attr = "lvl")
    8.   \-motifr::motifs_distribution(...)
    9.     \-pkg.env$sma$distributionMotifsAutoR(...)
   10.       \-reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  -- Error ('test-count_motifs.R:101:3'): exemplify_motif ------------------------
  <Rcpp::exception/C++Error/error/condition>
  Error: StopIteration
  
  Backtrace:
      x
   1. +-testthat::expect_null(...) at test-count_motifs.R:101:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-motifr::exemplify_motif(motifr::tidygraph_dummy_net, "1,2[I.B]")
   5.   \-pkg.env$sma$exemplifyMotif(py_g, motif)
   6.     \-reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  Error: Test failures
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   1.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/mpmi.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.5Mb
    libs   2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Error(s) in re-building vignettes:
--- re-building 'MSinference.Rnw' using knitr
Quitting from lines 250-271 (MSinference.Rnw) 
Error: processing vignette 'MSinference.Rnw' failed with diagnostics:
arguments imply differing number of rows: 0, 1
--- failed re-building 'MSinference.Rnw'

SUMMARY: processing the following file failed:
  'MSinference.Rnw'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [53s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mtdesign)
  > 
  > test_check("mtdesign")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  
  == Failed tests ================================================================
  -- Error ('test-obtainDesign.R:90:3'): obtainDesign works ----------------------
  Error in `dplyr::filter(., rSuccess < nTotal, rSuccess <= rTotal, rSuccess > 
      rFutility, rSuccess <= nStage1)`: i In argument: `rSuccess < nTotal`.
  Caused by error:
  ! cannot allocate vector of size 389.5 Mb
  Backtrace:
       x
    1. +-mtdesign::obtainDesign(...) at test-obtainDesign.R:90:2
    2. | +-base::do.call(...)
    3. | \-mtdesign::createGrid(p0 = 0.2, p1 = 0.4, alpha = 0.1, beta = 0.1)
    4. |   \-d %>% ...
    5. +-dplyr::filter(...)
    6. +-dplyr:::filter.data.frame(...)
    7. | \-dplyr:::filter_rows(.data, dots, by)
    8. |   \-dplyr:::filter_eval(...)
    9. |     +-base::withCallingHandlers(...)
   10. |     \-mask$eval_all_filter(dots, env_filter)
   11. |       \-dplyr (local) eval()
   12. \-base::.handleSimpleError(...)
   13.   \-dplyr (local) h(simpleError(msg, call))
   14.     \-rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown
pandoc.exe: Unknown extension: smart
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
pandoc document conversion failed with error 7
--- failed re-building 'tutorial.Rmd'

SUMMARY: processing the following file failed:
  'tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'leukemiasEset'
Error(s) in re-building vignettes:
--- re-building 'Tutorial.Rmd' using rmarkdown
Quitting from lines 131-144 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
there is no package called 'leukemiasEset'
--- failed re-building 'Tutorial.Rmd'

SUMMARY: processing the following file failed:
  'Tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  12.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.1Mb
    libs   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'asreml'
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Malformed Description field: should contain one or more complete sentences.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     4.8Mb
    models   1.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'neighbours.Rnw' using Sweave
Loading required namespace: NMOF
Loading required namespace: quadprog
Warning in par(old.par) : graphical parameter "cin" cannot be set
Warning in par(old.par) : graphical parameter "cra" cannot be set
Warning in par(old.par) : graphical parameter "csi" cannot be set
Warning in par(old.par) : graphical parameter "cxy" cannot be set
Warning in par(old.par) : graphical parameter "din" cannot be set
Warning in par(old.par) : graphical parameter "page" cannot be set
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "neighbours.tex" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'neighbours.Rnw' failed with diagnostics:
running 'texi2dvi' on 'neighbours.tex' failed

LaTeX errors:
! LaTeX Error: File `libertinus.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)


--- failed re-building 'neighbours.Rnw'

SUMMARY: processing the following file failed:
  'neighbours.Rnw'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.1/NestedCategBayesImpute.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Packages required and available but unsuitable versions: 'stats', 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/networkscaleup.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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    extdata   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.8Mb
    R         6.2Mb
    include   5.8Mb
    libs      2.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions: 'rxode2', 'rxode2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required and available but unsuitable version: 'rxode2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
Quitting from lines 41-45 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_i = a_i \, \mod 
                             \, m_i, \quad 1 \le i \le n 
l.560 ...i \, \mod \, m_i, \quad 1 \le i \le n }{}
                                                  
! Undefined control sequence.
<argument> a_i = a_j \, \mod 
                             \, \gcd (m_i, m_j)
l.564 \deqn{a_i = a_j \, \mod \, \gcd(m_i, m_j)}{}
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'occupationMeasurement-Ex.R' failed
The error most likely occurred in:

> ### Name: load_kldb_raw
> ### Title: Clean & Load KldB 2010 dataset.
> ### Aliases: load_kldb_raw load_kldb
> 
> ### ** Examples
> 
> # We recommend using a non-temporary directory for caching, so data is
> # downloaded only once and not time and time again
> cache_dir <- tempdir()
> # Note: The dataset will be downloaded from the internet
> # Load the cleaned dataset
> load_kldb(cache_dir = cache_dir)
[1] "Using a modified version of the KldB 2010.\nPlease mind the terms of use of the original KldB dataset (German):\n\n    (c) Statistik der Bundesagentur für Arbeit\n    Sie können Informationen speichern, (auch auszugsweise) mit Quellenangabe\n    weitergeben, vervielfältigen und verbreiten. Die Inhalte dürfen nicht\n    verändert oder verfälscht werden. Eigene Berechnungen sind erlaubt, jedoch\n    als solche kenntlich zu machen. Im Falle einer Zugänglichmachung im\n    Internet soll dies in Form einer Verlinkung auf die Homepage der Statistik\n    der Bundesagentur für Arbeit erfolgen. Die Nutzung der Inhalte für\n    gewerbliche Zwecke, ausgenommen Presse, Rundfunk und Fernsehen und\n    wissenschaftliche Publikationen, bedarf der Genehmigung durch die Statistik\n    der Bundesagentur für Arbeit.\n  "
trying URL 'https://www.klassifikationsserver.de/klassService/jsp/variant/downloadexport?type=EXPORT_CSV_VARIANT&variant=kldb2010&language=DE'
Warning in utils::download.file(url, destfile = kldb_archive_path, mode = "wb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in utils::download.file(url, destfile = kldb_archive_path, mode = "wb") : 
  cannot open URL 'https://www.klassifikationsserver.de/klassService/jsp/variant/downloadexport?type=EXPORT_CSV_VARIANT&variant=kldb2010&language=DE'
Calls: load_kldb -> load_kldb_raw -> <Anonymous>
Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(occupationMeasurement)
  > 
  > test_check("occupationMeasurement")
  Initiating curl with CURL_SSL_BACKEND: openssl
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 35 ]
  
  == Skipped tests ===============================================================
  * On CRAN (21)
  
  == Failed tests ================================================================
  -- Failure ('test-api.R:155:3'): endpoint '/v1/suggestions' works (for KldB) ---
  r$status_code (`actual`) not equal to 200 (`expected`).
  
    `actual`: 500
  `expected`: 200
  
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 35 ]
  Error: Test failures
  Execution halted
installed size is  9.4Mb
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    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.0Mb
    libs   2.6Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'library' or 'require' call not declared from: 'name'
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Using_ogrdbstats.Rmd' using rmarkdown
Error: processing vignette 'Using_ogrdbstats.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'Using_ogrdbstats.Rmd'

SUMMARY: processing the following file failed:
  'Using_ogrdbstats.Rmd'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'ohsome.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
Quitting from lines 290-298 (ohsome.Rmd) 
Error: processing vignette 'ohsome.Rmd' failed with diagnostics:
no applicable method for 'ohsome_boundary' applied to an object of class "data.frame"
--- failed re-building 'ohsome.Rmd'

SUMMARY: processing the following file failed:
  'ohsome.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> [0,\text 
                    {min}(p_1,p_2))
l.75 a number in \eqn{[0,\text{min}(p_1,p_2))}{}
                                                , indicating the cross-secti...
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Package suggested but not available for checking: 'cmdstanr'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.5Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'unix'
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          2.6Mb
GNU make is a SystemRequirements.
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs   24.5Mb
    share  10.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.5Mb
    libs     8.2Mb
    models   4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: 'openNLPmodels.en'
Found the following significant warnings:
  Warning: replacing previous import 'GPArotation::equamax' by 'psych::equamax' when loading 'OpenRepGrid'
  Warning: replacing previous import 'GPArotation::varimin' by 'psych::varimin' when loading 'OpenRepGrid'
See 'd:/Rcompile/CRANpkg/local/4.1/OpenRepGrid.Rcheck/00install.out' for details.
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   1.3Mb
    libs      2.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.8Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'rrelaxiv'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.1Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   2.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Initiating curl with CURL_SSL_BACKEND: openssl
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'owidR-Ex.R' failed
The error most likely occurred in:

> ### Name: owid_plot
> ### Title: Plot an owid dataset
> ### Aliases: owid_plot
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> human_rights <- owid("human-rights-scores")
Initiating curl with CURL_SSL_BACKEND: openssl
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: owid ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
--- re-building 'basic-usage.Rmd' using rmarkdown
trying URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
Content type 'application/zip' length 4396004 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
OxCal v4.4.4 (c) Bronk Ramsey (2021)
MCMC analysis
Sort	Burn	Trial	Save	Shrink	kPasses	Done	Ok	Convergence
[.]	[.]	[.]	[.]		3.0	10.0	100.0	100.0
[.]	[.]	[.]	[.]		6.0	20.0	100.0	70.4
[.]	[.]	[.]	[.]		12.0	22.2	100.0	84.8
[.]	[.]	[.]	[.]	[.]	24.0	22.2	100.0	91.2
[.]	[.]	[.]	[.]		48.0	22.2	100.0	93.5
[.]	[.]	[.]	[.]		96.0	22.2	100.0	97.2
[.]	[.]	[.]	[.]		144.0	33.3	100.0	97.2
[.]	[.]	[.]	[.]		192.0	44.4	100.0	97.2
[.]	[.]	[.]	[.]		240.0	55.6	100.0	97.2
[.]	[.]	[.]	[.]		288.0	66.7	100.0	97.2
[.]	[.]	[.]	[.]		336.0	77.8	100.0	97.2
[.]	[.]	[.]	[.]		384.0	88.9	100.0	97.2
[.]	[.]	[.]	[.]		432.0	100.0	100.0	97.2
[.]	[.]	[.]	[.]		480.0	111.1	100.0	97.2
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'basic-usage.Rmd'

SUMMARY: processing the following file failed:
  'basic-usage.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.3Mb
    libs   2.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    library  30.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'overview.Rmd' using rmarkdown
Error: processing vignette 'overview.Rmd' failed with diagnostics:
object 'preview_math' not found
--- failed re-building 'overview.Rmd'

SUMMARY: processing the following file failed:
  'overview.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'PS1_Cat.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'PS1_Cat.Rmd'

--- re-building 'PS1_Images.Rmd' using rmarkdown
Quitting from lines 29-33 (PS1_Images.Rmd) 
Error: processing vignette 'PS1_Images.Rmd' failed with diagnostics:
error:14077410:SSL routines:SSL23_GET_SERVER_HELLO:sslv3 alert handshake failure
--- failed re-building 'PS1_Images.Rmd'

SUMMARY: processing the following file failed:
  'PS1_Images.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(parsnip)
  > 
  > test_check("parsnip")
  
  This application has requested the Runtime to terminate it in an unusual way.
  Please contact the application's support team for more information.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'pastclim-Ex.R' failed
The error most likely occurred in:

> ### Name: var_labels
> ### Title: Generate pretty variable labels for plotting
> ### Aliases: var_labels
> 
> ### ** Examples
> 
> var_labels("bio01", dataset = "Example")
expression("annual mean temperature (" * degree * C * ")")
> 
> # set the data_path for this example to run on CRAN
> # users don't need to run this line
> set_data_path_for_CRAN()
[1] TRUE
> 
> # for a SpatRaster
> climate_20k <- region_slice(
+ time_bp = -20000,
+ bio_variables = c("bio01", "bio10", "bio12"),
+ dataset = "Example"
+ )
> terra::plot(climate_20k, main = var_labels(climate_20k, dataset = "Example"))
Error in x$main != "" : comparison is not allowed for expressions
Calls: <Anonymous> ... plot -> plot -> .local -> .prep.plot.data -> .plotit
Execution halted
Error(s) in re-building vignettes:
--- re-building 'a0_pastclim_overview.Rmd' using rmarkdown
Quitting from lines 313-314 (a0_pastclim_overview.Rmd) 
Error: processing vignette 'a0_pastclim_overview.Rmd' failed with diagnostics:
comparison is not allowed for expressions
--- failed re-building 'a0_pastclim_overview.Rmd'

--- re-building 'a1_available_datasets.Rmd' using rmarkdown
--- finished re-building 'a1_available_datasets.Rmd'

--- re-building 'a2_custom_datasets.Rmd' using rmarkdown
--- finished re-building 'a2_custom_datasets.Rmd'

SUMMARY: processing the following file failed:
  'a0_pastclim_overview.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   2.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   2.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.9Mb
Malformed Description field: should contain one or more complete sentences.
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/pcFactorStan.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs   13.6Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'PeakSegJoint-Ex.R' failed
The error most likely occurred in:

> ### Name: PeakSegJointError
> ### Title: PeakSegJointError
> ### Aliases: PeakSegJointError
> 
> ### ** Examples
> 
> 
> library(PeakSegJoint)
> data(H3K36me3.TDH.other.chunk1, envir=environment())
> lims <- c(43000000, 43200000) # left
> some.counts <-
+   subset(H3K36me3.TDH.other.chunk1$counts,
+          lims[1] < chromEnd & chromStart < lims[2])
> some.regions <-
+   subset(H3K36me3.TDH.other.chunk1$regions,
+          lims[1] < chromEnd & chromStart < lims[2])
> fit <- PeakSegJointSeveral(some.counts)
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > suite <- Sys.getenv("TEST_SUITE")
  > if(suite=="")suite <- NULL
  > test_check("PeakSegJoint", filter=suite)
  Loading required package: PeakSegJoint
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   4.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pedtools)
  > 
  > test_check("pedtools")
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 588 ]
  
  == Skipped tests ===============================================================
  * Identity examples - takes long time (1)
  * TODO: Mendelian check for X sibships (1)
  
  == Failed tests ================================================================
  -- Failure ('test-founder-inbreeding.R:24:3'): setFounderInbreeding works on lists --
  fi(y1) not equal to c(`1` = 1, `2` = 1, `4` = 1).
  3/3 mismatches (average diff: 1)
  [1] 0 - 1 == -1
  [2] 0 - 1 == -1
  [3] 0 - 1 == -1
  -- Failure ('test-founder-inbreeding.R:27:3'): setFounderInbreeding works on lists --
  fi(y2) not equal to c(`1` = 0, `2` = 1, `4` = 0).
  1/3 mismatches
  [2] 0 - 1 == -1
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 588 ]
  Error: Test failures
  Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
GNU make is a SystemRequirements.
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11882 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11882 (sockconn)
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/pense.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dendextendRcpp'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Note: possible error in 'simplify2array(msg, except = 0L)': unused argument (except = 0) 
See 'd:/Rcompile/CRANpkg/local/4.1/personalized.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
xgb_cv_personalized: possible error in simplify2array(msg, except =
  0L): unused argument (except = 0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
at_trans : <anonymous>: no visible global function definition for
  'viewportTransform'
at_trans : <anonymous>: no visible global function definition for
  'groupShear'
at_trans : <anonymous>: no visible global function definition for
  'groupFlip'
grobCoords.pp_grobCoords: no visible global function definition for
  'emptyGrobCoords'
grobCoords.pp_ps_transformation: no visible global function definition
  for 'emptyGrobCoords'
makeContent.pp_transformation: no visible global function definition
  for 'defineGrob'
makeContent.pp_transformation: no visible global function definition
  for 'useGrob'
transformationGrob: no visible binding for global variable
  'viewportTransform'
xylists_to_grobcoords: no visible global function definition for
  'emptyGrobCoords'
xylists_to_grobcoords: no visible global function definition for
  'gridCoords'
xylists_to_grobcoords : <anonymous>: no visible global function
  definition for 'gridCoords'
xylists_to_grobcoords: no visible global function definition for
  'gridGrobCoords'
Undefined global functions or variables:
  defineGrob emptyGrobCoords gridCoords gridGrobCoords groupFlip
  groupShear useGrob viewportTransform
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggsubplot'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    bin    8.6Mb
    doc    1.2Mb
    libs   1.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Packages suggested but not available for checking:
  'monocle3', 'ProjecTILs', 'SeuratWrappers'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: 'fs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2010)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
Package suggested but not available for checking: 'pollimetrydata'
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Running examples in 'PolygonSoup-Ex.R' failed
The error most likely occurred in:

> ### Name: toRGL
> ### Title: Conversion to 'rgl' mesh
> ### Aliases: toRGL
> 
> ### ** Examples
> 
> library(PolygonSoup)
> library(rgl)
> mesh <- Mesh(
+   truncatedIcosahedron[["vertices"]], truncatedIcosahedron[["faces"]],
+   triangulate = TRUE
+ )
â Processing mesh...
Successful polygon orientation.
The mesh is not triangle; no way to ensure it bounds a volume and whether it is outward oriented.
The mesh is closed.
Triangulation.
The mesh bounds a volume.
... done.

> rglmesh <- toRGL(mesh, segments = t(mesh[["edges"]]))
> open3d(windowRect = c(50, 50, 562, 562), zoom = 0.9)
wgl 
  6 
> shade3d(rglmesh, color = "darkred")
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:rgl'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.83 0.25 4.81 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   2.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      2.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(popsom)
  > 
  > test_check("popsom")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  == Failed tests ================================================================
  -- Failure ('test-predict.R:12:3'): map.predict function works -----------------
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  -- Failure ('test-predict.R:13:3'): map.predict function works -----------------
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(popsom)
  > 
  > test_check("popsom")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  
  == Failed tests ================================================================
  -- Failure ('test-predict.R:12:3'): map.predict function works -----------------
  p[56, 1] (`actual`) not equal to "versicolor" (`expected`).
  
  `actual`:   "virginica" 
  `expected`: "versicolor"
  -- Failure ('test-predict.R:13:3'): map.predict function works -----------------
  p[145, 1] (`actual`) not equal to "virginica" (`expected`).
  
  `actual`:   "versicolor"
  `expected`: "virginica" 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'Loading_and_manipulating.Rmd' using rmarkdown
Error: processing vignette 'Loading_and_manipulating.Rmd' failed with diagnostics:
Using anchor_sections requires Pandoc 2.0+
--- failed re-building 'Loading_and_manipulating.Rmd'

--- re-building 'full_pattern_summation.Rmd' using rmarkdown
Error: processing vignette 'full_pattern_summation.Rmd' failed with diagnostics:
Using anchor_sections requires Pandoc 2.0+
--- failed re-building 'full_pattern_summation.Rmd'

SUMMARY: processing the following files failed:
  'Loading_and_manipulating.Rmd' 'full_pattern_summation.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> \hat d:=\underset 
                             {|d|<0.5}{\mathrm {argmin}}\bigg \{\sum _{h=s}^...
l.88 ...d)}h^{2d-1}\bigg|^r\bigg\}, \quad r > 0}{}
                                                  .
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \to a}\fra...
l.269 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.271 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
! Undefined control sequence.
<argument> K_1 = \iint 
                       _{I^2}\frac {1}{l_0(u)l_n(v)}\lim _{\theta \rightarro...
l.469 ...{\theta}(u,v)}{\partial\theta}\,dudv, }{}
                                                  
! Undefined control sequence.
<argument> \{F_n\}_{n\in \mathbb 
                                 {N}}
l.472 \eqn{\{F_n\}_{n\in\mathbb{N}}}{}
                                       is a sequence of absolutely continuou...
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   3.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.963 ...m_{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1138 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
                                                  
! Undefined control sequence.
<argument> ...1}^{C+1} \hat {\sigma }^2_c}, \text 
                                                  { } \hat {\mu } + q^{calib...
l.1289 ..._{c=1}^{C+1} \hat{\sigma}^2_c} \Big].}{}
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.8Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI', 'highs'
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    4.5Mb
    libs   3.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
Running examples in 'processmapR-Ex.R' failed
The error most likely occurred in:

> ### Name: trace_explorer
> ### Title: Trace Explorer
> ### Aliases: trace_explorer trace_explorer.eventlog
> ###   trace_explorer.activitylog
> 
> ### ** Examples
> 
> library(processmapR)
> library(eventdataR)
> 
> patients %>%
+  trace_explorer(coverage = 0.8)
Error in `:=`("case_classifier", !!case_id_(log)) : 
  Check that is.data.table(DT) == TRUE. Otherwise, := and `:=`(...) are defined for use in j, once only and in particular ways. See help(":=").
Calls: %>% ... arrange -> as.data.frame -> rename -> rename.log -> :=
Execution halted
Running examples in 'processmapR-Ex.R' failed
The error most likely occurred in:

> ### Name: trace_explorer
> ### Title: Trace Explorer
> ### Aliases: trace_explorer trace_explorer.eventlog
> ###   trace_explorer.activitylog
> 
> ### ** Examples
> 
> library(processmapR)
> library(eventdataR)
> 
> patients %>%
+  trace_explorer(coverage = 0.8)
Error in `:=`("case_classifier", !!case_id_(log)) : 
  Check that is.data.table(DT) == TRUE. Otherwise, := and `:=`(...) are defined for use in j, once only and in particular ways. See help(":=").
Calls: %>% ... arrange -> as.data.frame -> rename -> rename.log -> :=
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/projpred.Rcheck/00install.out' for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.3Mb
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rdt'
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'prt-Ex.R' failed
The error most likely occurred in:

> ### Name: print.prt
> ### Title: Printing prt
> ### Aliases: print.prt format.prt trunc_dt
> 
> ### ** Examples
> 
> cars <- as_prt(mtcars)
> 
> print(cars)
Error:
! `colonnade()` was deprecated in pillar 1.9.0 and is now defunct.
i Please use `tbl_format_setup()` instead.
Backtrace:
     x
  1. +-base::print(cars)
  2. \-prt:::print.prt(cars)
  3.   +-prt:::cat_line(format(x, ..., n = n, width = width, max_extra_cols = max_extra_cols))
  4.   | +-base::trimws(paste0(...), "right")
  5.   | | \-base (local) mysub(paste0(whitespace, "+$"), x)
  6.   | |   \-base::sub(re, "", x, perl = TRUE)
  7.   | |     \-base::is.factor(x)
  8.   | \-base::paste0(...)
  9.   +-base::format(x, ..., n = n, width = width, max_extra_cols = max_extra_cols)
 10.   \-prt:::format.prt(x, ..., n = n, width = width, max_extra_cols = max_extra_cols)
 11.     +-base::format(trunc_dt(x, n = n, width = width, max_extra_cols = max_extra_cols))
 12.     \-prt::trunc_dt(x, n = n, width = width, max_extra_cols = max_extra_cols)
 13.       \-prt:::shrink_dt(df, rows)
 14.         \-pillar::colonnade(df, has_row_id = FALSE)
 15.           \-lifecycle::deprecate_stop("1.9.0", "pillar::colonnade()", "pillar::tbl_format_setup()")
 16.             \-lifecycle:::deprecate_stop0(msg)
 17.               \-rlang::cnd_signal(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'prt.Rmd' using rmarkdown
Quitting from lines 35-37 (prt.Rmd) 
Error: processing vignette 'prt.Rmd' failed with diagnostics:
`colonnade()` was deprecated in pillar 1.9.0 and is now defunct.
i Please use `tbl_format_setup()` instead.
--- failed re-building 'prt.Rmd'

SUMMARY: processing the following file failed:
  'prt.Rmd'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: 'splines'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/PST.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.5Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.1/pulseTD.Rcheck/
vign_test/pulseTD/vignettes/tutorial_files/figure-latex/plotRatest,any\%20time-
1.pdf' not found.

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/pulseTD.Rcheck/vign_test/pulseTD/vignettes/tutorial.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See tutorial.log for more info.
--- failed re-building 'tutorial.Rmd'

SUMMARY: processing the following file failed:
  'tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    libs         1.3Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
NB: this package is only installed for sub-architecture 'x64'
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      5.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   2.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.9Mb
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Error(s) in re-building vignettes:
--- re-building 'textmodel_performance.Rmd' using rmarkdown
Quitting from lines 32-39 (textmodel_performance.Rmd) 
Error: processing vignette 'textmodel_performance.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'textmodel_performance.Rmd'

SUMMARY: processing the following file failed:
  'textmodel_performance.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc         2.9Mb
    shiny_app   1.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! pdfTeX error (ext4): \pdfendlink ended up in different nesting level than \pd
fstartlink.
\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1 \begin{theindex}
!  ==> Fatal error occurred, no output PDF file produced!
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/r2sundials.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/ranger.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(Rapp)
  > 
  > test_check("Rapp")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  
  == Failed tests ================================================================
  -- Failure ('test-basics.R:21:3'): examples work -------------------------------
  run_app("unique.R", input = c("a", "b", "c", "c", "b", "a")) (`actual`) not equal to c("a", "b", "c") (`expected`).
  
  `actual`:              
  `expected`: "a" "b" "c"
  -- Failure ('test-basics.R:26:3'): examples work -------------------------------
  run_app(...) (`actual`) not equal to c("c", "b", "a") (`expected`).
  
  `actual`:              
  `expected`: "c" "b" "a"
  -- Failure ('test-basics.R:36:3'): examples work -------------------------------
  run_app("unique.R", fi) (`actual`) not equal to c("a", "b", "c") (`expected`).
  
  `actual`:              
  `expected`: "a" "b" "c"
  -- Failure ('test-basics.R:41:3'): examples work -------------------------------
  run_app("unique.R", "--from-last", fi) (`actual`) not equal to c("c", "b", "a") (`expected`).
  
  `actual`:              
  `expected`: "c" "b" "a"
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.1Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rayshader.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
--- re-building 'rblpapi-intro.md' using mdweave_to_html
Error: processing vignette 'rblpapi-intro.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'rblpapi-intro.md'

SUMMARY: processing the following file failed:
  'rblpapi-intro.md'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Running 'test-all.R' [59s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(rcites)
  > library(tibble)
  > test_check("rcites")
  Initiating curl with CURL_SSL_BACKEND: openssl
  v Token stored for the session.
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 105 ]
  
  == Skipped tests ===============================================================
  * On CRAN (6)
  
  == Failed tests ================================================================
  -- Failure ('test-distributions.R:44:5'): spp_distributions() language works ---
  lang_GQ %in% res1$distributions$name (`actual`) not identical to c(FALSE, TRUE, FALSE) (`expected`).
  
  `actual`:   FALSE FALSE FALSE
  `expected`: FALSE TRUE  FALSE
  -- Failure ('test-legislations.R:47:5'): spp_cites_legislation() scope & language works --
  "Guinée" %in% res$cites_suspensions$geo_entity.name is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 105 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
    po    2.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error(s) in re-building vignettes:
--- re-building 'binnmuAfterR340.md' using mdweave_to_html
Error: processing vignette 'binnmuAfterR340.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'binnmuAfterR340.md'

SUMMARY: processing the following file failed:
  'binnmuAfterR340.md'

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      2.3Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    include  44.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    lib       4.6Mb
GNU make is a SystemRequirements.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      2.6Mb
Found the following significant warnings:
  ../windows/hiredis-1.0.0/include/hiredis/sds.h:53:14: warning: ISO C++ forbids flexible array member 'buf' [-Wpedantic]
  ../windows/hiredis-1.0.0/include/hiredis/sds.h:59:14: warning: ISO C++ forbids flexible array member 'buf' [-Wpedantic]
  ../windows/hiredis-1.0.0/include/hiredis/sds.h:65:14: warning: ISO C++ forbids flexible array member 'buf' [-Wpedantic]
  ../windows/hiredis-1.0.0/include/hiredis/sds.h:71:14: warning: ISO C++ forbids flexible array member 'buf' [-Wpedantic]
  ../windows/hiredis-1.0.0/include/hiredis/sds.h:77:14: warning: ISO C++ forbids flexible array member 'buf' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.1/RcppRedis.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/RcppSimdJson.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'introduction.md' using mdweave_to_html
Error: processing vignette 'introduction.md' failed with diagnostics:
Running '' had status 127; this generally means that '' could not be found. Make sure '' in on the path.
--- failed re-building 'introduction.md'

SUMMARY: processing the following file failed:
  'introduction.md'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rcrypt.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'R.devices-overview.tex.rsp' using rsp
R.devices v2.17.1 (2022-06-21 08:00:02 UTC) successfully loaded. See ?R.devices for help.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "R.devices-overview.tex" --max-iterations=20 -I "d:/RCompile/CRANpkg/local/4.1/R.devices.Rcheck/vign_test/R.devices/vignettes" -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'R.devices-overview.tex.rsp' failed with diagnostics:
running 'texi2dvi' on 'R.devices-overview.tex' failed

LaTeX errors:
devices-overview.tex:55: LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help
You're in trouble here.  Try typing  <return>  to proceed.

--- failed re-building 'R.devices-overview.tex.rsp'

SUMMARY: processing the following file failed:
  'R.devices-overview.tex.rsp'

Error: Vignette re-building failed.
Execution halted
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/RDieHarder.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   1.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dataui'
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(readODS)
  > test_check("readODS")
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 167 ]
  
  == Skipped tests ===============================================================
  * On CRAN (8)
  
  == Failed tests ================================================================
  -- Error ('test_xml_fuzz.R:6:5'): basic test case #1 ---------------------------
  Error in `read_xml.character(con, options = c("NOBLANKS", "HUGE"))`: Input is not proper UTF-8, indicate encoding !
  Bytes: 0x9A 0x22 0x20 0x74 [9]
  Backtrace:
      x
   1. \-readODS::read_ods(ascii_test_file) at test_xml_fuzz.R:6:4
   2.   \-readODS:::.parse_ods_to_sheets(path)
   3.     \-readODS:::.parse_ods_file(file)
   4.       +-xml2::read_xml(con, options = c("NOBLANKS", "HUGE"))
   5.       \-xml2:::read_xml.character(con, options = c("NOBLANKS", "HUGE"))
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 167 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/recometrics.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
Error(s) in re-building vignettes:
--- re-building 'FWE_distribution.Rmd' using rmarkdown
--- finished re-building 'FWE_distribution.Rmd'

--- re-building 'OW_distribution.Rmd' using rmarkdown
Quitting from lines 218-225 (OW_distribution.Rmd) 
Error: processing vignette 'OW_distribution.Rmd' failed with diagnostics:
unused arguments (title.font, seg.len)
--- failed re-building 'OW_distribution.Rmd'

SUMMARY: processing the following file failed:
  'OW_distribution.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Initiating curl with CURL_SSL_BACKEND: openssl
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'repoRter_nih.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
! Undefined control sequence.
l.68 \UseRawInputEncoding

Error: processing vignette 'repoRter_nih.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.1/repoRter.nih.Rcheck/vign_test/repoRter.nih/vignettes/repoRter_nih.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See repoRter_nih.log for more info.
--- failed re-building 'repoRter_nih.Rmd'

SUMMARY: processing the following file failed:
  'repoRter_nih.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode char â (U+2011)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs      2.5Mb
    swagger   1.4Mb
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      3.2Mb
    models    1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/Rfast2.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/Rforestry.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 112.7Mb
  sub-directories of 1Mb or more:
    doc        3.7Mb
    gdal       2.2Mb
    libs      94.3Mb
    pictures   1.3Mb
    proj       8.7Mb
Error(s) in re-building vignettes:
--- re-building 'CRS_projections_transformations.Rmd' using rmarkdown
Quitting from lines 330-331 (CRS_projections_transformations.Rmd) 
Error: processing vignette 'CRS_projections_transformations.Rmd' failed with diagnostics:
failure in points 1
--- failed re-building 'CRS_projections_transformations.Rmd'

--- re-building 'PROJ6_GDAL3.Rmd' using rmarkdown
--- finished re-building 'PROJ6_GDAL3.Rmd'

--- re-building 'OGR_shape_encoding.Rnw' using Sweave
Loading required package: sp
Please note that rgdal will be retired during 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.
See https://r-spatial.org/r/2022/04/12/evolution.html and https://github.com/r-spatial/evolution
rgdal: version: 1.6-5, (SVN revision 1199)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.4.1, released 2021/12/27
Path to GDAL shared files: D:/temp/RtmpApG2IV/RLIBS_93cc637f75b8/rgdal/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: D:/temp/RtmpApG2IV/RLIBS_93cc637f75b8/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.6-0
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
Warning: OGR support is provided by the sf and terra packages among others
Warning: OGR support is provided by the sf and terra packages among others
Warning: OGR support is provided by the sf and terra packages among others
Warning: OGR support is provided by the sf and terra packages among others
Read 1 item
--- finished re-building 'OGR_shape_encoding.Rnw'

SUMMARY: processing the following file failed:
  'CRS_projections_transformations.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.1/rgl.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Running examples in 'Rgof-Ex.R' failed
The error most likely occurred in:

> ### Name: gof_power_disc
> ### Title: Find the power of various gof tests for discrete data.
> ### Aliases: gof_power_disc
> 
> ### ** Examples
> 
> # Power of tests when null hypothesis specifies a binomial N=10, p=0.5 distribution but 
> # true data comes from a binomial distribution with success probability 0.55 or 0.6.
> vals=0:10
> pnull = function() pbinom(0:10, 10, 0.5)
> rnull = function() table(c(0:10, rbinom(1000, 10, 0.5)))-1
> ralt = function(p) table(c(0:10, rbinom(1000, 10, p)))-1
> gof_power_disc(pnull, rnull, vals, ralt, c(0.515, 0.53), B=c(500, 500))
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Initiating curl with CURL_SSL_BACKEND: openssl
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Initiating curl with CURL_SSL_BACKEND: openssl
Running examples in 'ricu-Ex.R' failed
The error most likely occurred in:

> ### Name: transform_fun
> ### Title: Item callback utilities
> ### Aliases: transform_fun binary_op comp_na set_val apply_map convert_unit
> 
> ### ** Examples
> 
> dat <- ts_tbl(x = rep(1:2, each = 5), y = hours(rep(1:5, 2)), z = 1:10)
> 
> subtract_3 <- transform_fun(binary_op(`-`, 3))
> subtract_3(data.table::copy(dat), val_var = "z")
Error:
! `colonnade()` was deprecated in pillar 1.9.0 and is now defunct.
i Please use `tbl_format_setup()` instead.
Backtrace:
     x
  1. +-base (local) `<fn>`(x)
  2. \-ricu:::print.id_tbl(x)
  3.   +-ricu:::cat_line(format(x, ..., n = n, width = width))
  4.   | +-base::trimws(paste0(...), "right")
  5.   | | \-base (local) mysub(paste0(whitespace, "+$"), x)
  6.   | |   \-base::sub(re, "", x, perl = TRUE)
  7.   | |     \-base::is.factor(x)
  8.   | \-base::paste0(...)
  9.   +-base::format(x, ..., n = n, width = width)
 10.   \-ricu:::format.id_tbl(x, ..., n = n, width = width)
 11.     +-base::format(prt::trunc_dt(x, n = n, width = width))
 12.     \-prt::trunc_dt(x, n = n, width = width)
 13.       \-prt:::shrink_dt(df, rows)
 14.         \-pillar::colonnade(df, has_row_id = FALSE)
 15.           \-lifecycle::deprecate_stop("1.9.0", "pillar::colonnade()", "pillar::tbl_format_setup()")
 16.             \-lifecycle:::deprecate_stop0(msg)
 17.               \-rlang::cnd_signal(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'jss.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
Quitting from lines 452-455 (jss.Rmd) 
Error: processing vignette 'jss.Rmd' failed with diagnostics:
`colonnade()` was deprecated in pillar 1.9.0 and is now defunct.
i Please use `tbl_format_setup()` instead.
--- failed re-building 'jss.Rmd'

--- re-building 'ricu.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'ricu.Rmd'

--- re-building 'uom.Rmd' using rmarkdown
Initiating curl with CURL_SSL_BACKEND: openssl
--- finished re-building 'uom.Rmd'

SUMMARY: processing the following file failed:
  'jss.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.3Mb
Initiating curl with CURL_SSL_BACKEND: openssl
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory