installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

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
Unknown package ‘btergm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   4.8Mb
    help   1.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'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  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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 28.9Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs   25.6Mb
'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 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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
    libs      1.0Mb
'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'
Running examples in ‘ridge-Ex.R’ failed
The error most likely occurred in:

> ### Name: pvals
> ### Title: Compute p-values for ridgeLinear and ridgeLogistic models
> ### Aliases: pvals pvals.ridgeLinear pvals.ridgeLogistic
> ###   plot.pvalsRidgeLinear plot.pvalsRidgeLogistic print.pvalsRidgeLinear
> ###   print.pvalsRidgeLogistic
> 
> ### ** Examples
> 
> data(GenBin)
> mod <- logisticRidge(Phenotypes ~ ., data = as.data.frame(GenBin))

Execution halted
Specified C++11: please drop specification unless essential
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.0Mb
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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
'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.
Re-running with no redirection of stdout/stderr.
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 nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Package suggested but not available for checking: ‘portfolioBacktest’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
'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-x86_64/results/4.3/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 nor [v]sprintf. 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.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.0Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.7Mb
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 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.0Mb
'LazyData' is specified without a 'data' directory
installed size is 165.9Mb
  sub-directories of 1Mb or more:
    libs  164.9Mb
GNU make is a SystemRequirements.
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    include   7.3Mb
    lib      37.8Mb
    libs     26.4Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rnaturalearthhires’
'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   8.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
installed size is 135.1Mb
  sub-directories of 1Mb or more:
    libs  134.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘bridgestan’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
GNU make is a SystemRequirements.
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Package suggested but not available for checking: ‘recount3’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    2.3Mb
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.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 120.9Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     118.7Mb
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'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 12.2Mb
  sub-directories of 1Mb or more:
    R  12.1Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
--- re-building ‘RobPer_vignette.Rnw’ using Sweave
Loading required package: robustbase
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Loading required package: splines
Loading required package: BB
Loading required package: rgenoud
##  rgenoud (Version 5.9-0.3, Build Date: 2022-04-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

Error: processing vignette 'RobPer_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'RobPer_vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 97.5Mb
  sub-directories of 1Mb or more:
    libs  96.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ivgets’
Package unavailable to check Rd xrefs: ‘ivgets’
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Specified C++11: please drop specification unless essential
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.1Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'car', 'HH'
Package unavailable to check Rd xrefs: ‘HH’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'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   5.6Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         3.7Mb
    extdata   2.7Mb
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
'LazyData' is specified without a 'data' directory
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MBESS’
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   8.3Mb
Package suggested but not available for checking: ‘RandomFields’
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 53.1Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 102.8Mb
  sub-directories of 1Mb or more:
    libs  102.2Mb
installed size is  5.6Mb
  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
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
Errors in running code in vignettes:
when running code in ‘Using.RRPP.Rmd’
  ...
> fit.par <- lm(fit$call$f1, data = fit$LM$data)

> all.equal(fit$LM$coefficients, fit.par$coefficients)
[1] TRUE

> summary(manova(fit.par))

  When sourcing ‘Using.RRPP.R’:
Error: residuals have rank 49 < 112
Execution halted

  ‘ANOVA.vs.MANOVA.Rmd’ using ‘UTF-8’... [28s/42s] OK
  ‘Using.RRPP.Rmd’ using ‘UTF-8’... failed
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fields', 'qgraph'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/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 ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘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 nor [v]sprintf. 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.
'LazyData' is specified without a 'data' directory
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installed size is 27.4Mb
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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
Package suggested but not available for checking: ‘gurobi’
installed size is  7.3Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘INLA’
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 299.3Mb
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GNU make is a SystemRequirements.
installed size is 96.4Mb
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GNU make is a SystemRequirements.
installed size is 58.4Mb
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GNU make is a SystemRequirements.
installed size is 50.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggpubr’
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installed size is 38.0Mb
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Specified C++11: please drop specification unless essential
installed size is 28.0Mb
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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
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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installed size is  5.0Mb
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installed size is 123.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 224.1Mb
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GNU make is a SystemRequirements.
Running examples in ‘RtsEva-Ex.R’ failed
The error most likely occurred in:

> ### Name: tsEstimateAverageSeasonality
> ### Title: Estimate Average Seasonality
> ### Aliases: tsEstimateAverageSeasonality
> 
> ### ** Examples
> 
> timeAndSeries <- ArdecheStMartin
> timeStamps <- ArdecheStMartin[,1]
> series  <- ArdecheStMartin[,2]
> timeWindow <- 30*365  # 30 years
> rs <- tsEvaDetrendTimeSeries(timeStamps, series, timeWindow)
> nRunMn <- rs@nRunMn
> cat("computing trend seasonality ...\n")
computing trend seasonality ...
> seasonalitySeries <- rs@detrendSeries
> result <- tsEstimateAverageSeasonality(timeStamps, seasonalitySeries, timeWindow=rs@nRunMn)
Warning in pracma::interp1(avgTmStamp, monthAvgVec, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
Warning in pracma::interp1(avgTmStamp, monthAvgVex, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
> plot(result$regime, type = "l", xlab = "Day", ylab = "Regime", main = "Estimated Regime")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  7.7Mb
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installed size is 11.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
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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
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘GSVAdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 48.6Mb
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Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
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installed size is 66.3Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.9Mb
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installed size is 10.8Mb
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Package suggested but not available for checking: ‘partykit’
Package unavailable to check Rd xrefs: ‘partykit’
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.2Mb
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installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
installed size is  5.5Mb
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    data   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
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installed size is 11.3Mb
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installed size is  9.0Mb
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Specified C++11: please drop specification unless essential
installed size is  9.5Mb
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Specified C++14: please drop specification unless essential
installed size is 10.3Mb
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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
installed size is 14.8Mb
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installed size is 12.3Mb
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Specified C++14: please drop specification unless essential
installed size is 38.0Mb
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checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lme4’
Note: skipping ‘my-vignette.Rnw’ due to unavailable dependencies: 'lme4'
installed size is 14.4Mb
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    libs  13.3Mb
Specified C++11: please drop specification unless essential
installed size is 20.5Mb
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checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 54.3Mb
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Specified C++11: please drop specification unless essential
installed size is 10.0Mb
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Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'car', 'ergm', 'networkTomography',
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'LazyData' is specified without a 'data' directory
installed size is 47.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    libs   5.1Mb
installed size is  6.3Mb
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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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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GNU make is a SystemRequirements.
installed size is  6.3Mb
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installed size is  7.2Mb
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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
installed size is  5.2Mb
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    R      1.0Mb
    libs   3.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
installed size is  8.2Mb
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    libs   7.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  8.8Mb
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    data   4.9Mb
    libs   3.6Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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   4.9Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Package suggested but not available for checking: ‘Linnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘batchelor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘simplifyEnrichment’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 32.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'batchelor', 'ReactomeGSA', 'celldex', 'SingleR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmGamPoi’
installed size is 21.2Mb
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Package suggested but not available for checking: ‘oligoClasses’
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'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
Package which this enhances but not available for checking: ‘glmGamPoi’
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using Sweave
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’

Attaching package: ‘scuba’

The following objects are masked _by_ ‘.GlobalEnv’:

    pedro902, pedro903, pedro904, pedro922, pedro943, pedro944,
    pedro945, pedro946, pedro948, pedro949, pedro950

Error: processing vignette 'intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \marginsize
               {2cm}{2cm}{2cm}{2cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘intro.Rnw’

SUMMARY: processing the following file failed:
  ‘intro.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  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R          3.0Mb
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installed size is 89.3Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sdmvspecies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Error(s) in re-building vignettes:
--- re-building ‘sealasso.Rnw’ using Sweave
Loading required package: lars
Loaded lars 1.3

Error: processing vignette 'sealasso.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sealasso.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \marginsize
               {2.5cm}{2.5cm}{2.5cm}{2.5cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sealasso.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R   8.6Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'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:
    R      2.0Mb
    libs  15.2Mb
GNU make is a SystemRequirements.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.6Mb
'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:
    data   2.9Mb
    libs   7.8Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
'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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpfr’
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'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   7.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is  5.4Mb
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installed size is  7.5Mb
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GNU make is a SystemRequirements.
installed size is  6.6Mb
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installed size is  9.4Mb
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Package suggested but not available for checking: ‘airway’
Packages suggested but not available for checking:
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installed size is 17.7Mb
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installed size is 19.9Mb
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GNU make is a SystemRequirements.
installed size is  7.3Mb
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Package suggested but not available for checking: ‘pwalign’
installed size is  5.8Mb
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GNU make is a SystemRequirements.
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installed size is 56.7Mb
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GNU make is a SystemRequirements.
installed size is 16.0Mb
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checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
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installed size is 11.2Mb
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installed size is  7.8Mb
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installed size is 14.1Mb
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Package suggested but not available for checking: ‘cmdstanr’
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installed size is  5.1Mb
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Package suggested but not available for checking: ‘edgeR’
Note: skipping ‘SIBER.Rnw’ due to unavailable dependencies: 'edgeR'
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Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.9Mb
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    help      1.7Mb
Packages suggested but not available for checking:
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installed size is  5.1Mb
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Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Package suggested but not available for checking: ‘rhdf5’
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
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installed size is  7.4Mb
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installed size is 18.6Mb
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installed size is  6.1Mb
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GNU make is a SystemRequirements.
installed size is 14.5Mb
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Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
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installed size is  5.7Mb
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Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘copula’
installed size is  5.0Mb
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Package suggested but not available for checking: ‘INLA’
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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installed size is 22.7Mb
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installed size is  5.4Mb
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    libs   2.8Mb
Problems with news in ‘NEWS.md’:
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installed size is 11.1Mb
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installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
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installed size is 13.1Mb
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Package which this enhances but not available for checking: ‘kmndirs’
installed size is  7.1Mb
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GNU make is a SystemRequirements.
installed size is 39.2Mb
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installed size is  5.6Mb
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installed size is  6.3Mb
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installed size is 33.1Mb
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installed size is  5.1Mb
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installed size is  5.9Mb
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Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
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checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘gurobi’
installed size is  5.8Mb
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GNU make is a SystemRequirements.
installed size is  5.3Mb
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checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
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installed size is  7.2Mb
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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installed size is  5.1Mb
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installed size is 16.7Mb
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
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Malformed Description field: should contain one or more complete sentences.
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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’
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    libs      2.8Mb
Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  5.2Mb
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installed size is  5.9Mb
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checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
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installed size is  6.0Mb
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installed size is 14.2Mb
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installed size is  7.7Mb
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installed size is  6.7Mb
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installed size is  5.4Mb
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installed size is 16.8Mb
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installed size is  5.6Mb
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installed size is  8.4Mb
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    libs      2.0Mb
installed size is 16.1Mb
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    libs      5.9Mb
installed size is  5.1Mb
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    libs   2.5Mb
installed size is  5.7Mb
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Package suggested but not available for checking: ‘NLMR’
installed size is  6.8Mb
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Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
installed size is 39.9Mb
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installed size is  5.1Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
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installed size is 15.1Mb
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S3 methods shown with full name in documentation object 'SparseM.ontology':
  ‘as.matrix.csr’ ‘is.matrix.csr’ ‘is.matrix.csc’ ‘is.matrix.ssr’
  ‘is.matrix.ssc’ ‘is.matrix.coo’

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
installed size is 47.6Mb
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Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/spaths.Rcheck/00install.out’ for details.
Package required but not available: ‘SpatialExperiment’

Package suggested but not available for checking: ‘HDF5Array’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 95.0Mb
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installed size is  5.8Mb
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installed size is  5.5Mb
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    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
Specified C++14: please drop specification unless essential
installed size is 14.1Mb
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    libs  12.5Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
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    libs   4.2Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
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installed size is  5.5Mb
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Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', '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.univar',
  '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.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.univar', '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.univar', '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  5.3Mb
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installed size is 23.1Mb
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    libs  22.2Mb
installed size is 13.4Mb
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    data   3.3Mb
    libs   9.5Mb
installed size is  6.3Mb
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    libs   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.6Mb
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    shapes   3.2Mb
installed size is  5.9Mb
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installed size is  9.7Mb
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Package suggested but not available for checking: ‘scRNAseq’
Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> ### Name: BWR
> ### Title: BW ratio calculation
> ### Aliases: BWR
> 
> ### ** Examples
> 
> res=makeSimulatedData();
> X=res$data;
> groupLabel=res$label;
> peakList <- detectSpecPeaks(X,
+                             nDivRange = c(128),
+                             scales = seq(1, 16, 2),
+                             baselineThresh = 50000,
+                             SNR.Th = -1,
+                             verbose=FALSE
+ );
> resFindRef<- findRef(peakList);
> refInd <- resFindRef$refInd;
> maxShift = 50;
> Y <- dohCluster(X,
+                 peakList = peakList,
+                 refInd = refInd,
+                 maxShift  = maxShift,
+                 acceptLostPeak = TRUE, verbose=FALSE);
Warning in min(peakList) :
  no non-missing arguments to min; returning Inf
Warning in max(peakList) :
  no non-missing arguments to max; returning -Inf
Error in startP:(minpeakList - 1) : result would be too long a vector
Calls: dohCluster -> .withMaxShift -> hClustAlign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:34.091 R[19637:2290508776] XType: Using static font registry.

Quitting from lines 111-120 [Spectral_alignment] (classic_speaq_vignette.Rmd)
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:40.223 R[20964:2290511430] XType: Using static font registry.

Quitting from lines 71-83 [detect winepeaks] (speaq2_illustrations.Rmd)
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    data   4.8Mb
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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.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is 19.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    libs   5.1Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
installed size is  5.9Mb
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    R      2.0Mb
    data   1.8Mb
    doc    1.5Mb
installed size is 17.3Mb
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Specified C++11: please drop specification unless essential
installed size is  7.2Mb
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    R      2.0Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
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    doc   7.6Mb
Package suggested but not available for checking: ‘ggraph’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.1Mb
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installed size is 50.2Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
  Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
  Backtrace:
      ▆
   1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:0
   2.   └─spsurv:::spbp.default(...)
   3.     └─spsurv:::spbp.mle(standata = standata, ...)
   4.       ├─rstan::optimizing(...)
   5.       └─rstan::optimizing(...)
   6.         └─rstan (local) .local(object, ...)
   7.           └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
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Package suggested but not available for checking: ‘ecpc’
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 41.8Mb
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    libs  40.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 127.1Mb
  sub-directories of 1Mb or more:
    libs  126.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘SSsimple.Snw’ using Sweave
Loading required package: mvtnorm
Error: processing vignette 'SSsimple.Snw' failed with diagnostics:
Running 'texi2dvi' on 'SSsimple.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SSsimple.Snw’

SUMMARY: processing the following file failed:
  ‘SSsimple.Snw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
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    libs   3.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 36.4Mb
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    libs  35.8Mb
installed size is 51.2Mb
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installed size is 17.4Mb
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    include  11.7Mb
    lib       3.7Mb
GNU make is a SystemRequirements.
installed size is 92.5Mb
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    libs  91.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.8Mb
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    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.8Mb
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    data   3.6Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  7.5Mb
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    libs      4.2Mb
installed size is  7.5Mb
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Package suggested but not available for checking: ‘asreml’
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tweedie’
Package unavailable to check Rd xrefs: ‘tweedie’
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    libs   4.4Mb
installed size is 25.4Mb
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checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 63.4Mb
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    libs   5.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘StMoMoVignette.Rnw’ using Sweave
Loading required package: gnm
Loading required package: forecast
Error: processing vignette 'StMoMoVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'StMoMoVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `ctable.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [caption = false]{subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'StMoMoVignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.2Mb
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    data   2.5Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
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    data   7.3Mb
installed size is 34.9Mb
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    libs  33.9Mb
installed size is  9.8Mb
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    doc    1.9Mb
    libs   6.9Mb
installed size is 46.7Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
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    libs   6.9Mb
installed size is 11.0Mb
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    libs  10.8Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
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Package suggested but not available for checking: ‘StrathE2E2examples’
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installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Package unavailable to check Rd xrefs: ‘HDoutliers’
installed size is 13.4Mb
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Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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    libs   6.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.6Mb
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    libs  33.7Mb
installed size is  9.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
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installed size is  5.4Mb
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Packages suggested but not available for checking: 'arm', 'caret', 'party'
Package required but not available: ‘GSVA’

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
Package suggested but not available for checking: ‘INLA’
installed size is  6.9Mb
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    doc    3.1Mb
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installed size is 15.5Mb
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Package suggested but not available for checking: ‘velocyto.R’
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  'arm', 'bartMachine', 'extraTrees', 'party', 'xgboost'
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/SurfRough.Rcheck/00install.out’ for details.
installed size is  6.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
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'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  7.0Mb
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    R     2.1Mb
    doc   2.3Mb
installed size is 64.9Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
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    data   3.0Mb
    doc    2.5Mb
installed size is  6.8Mb
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Package suggested but not available for checking: ‘gurobi’
installed size is 10.1Mb
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Packages suggested but not available for checking:
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installed size is 11.4Mb
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installed size is 65.0Mb
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GNU make is a SystemRequirements.
installed size is  8.5Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 46.9Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
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installed size is 22.1Mb
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installed size is 44.8Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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'LazyData' is specified without a 'data' directory
installed size is 22.7Mb
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'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/systemfonts.Rcheck/00install.out’ for details.
installed size is  6.2Mb
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Specified C++11: please drop specification unless essential
installed size is 11.9Mb
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    libs  11.4Mb
installed size is 10.3Mb
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    data   5.3Mb
    libs   4.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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installed size is 13.7Mb
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘dearseq’
Package unavailable to check Rd xrefs: ‘dearseq’
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installed size is  5.1Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  7.5Mb
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Specified C++11: please drop specification unless essential
installed size is 10.5Mb
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installed size is 38.5Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
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installed size is  7.4Mb
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Package which this enhances but not available for checking: ‘R2wd’
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 17.9Mb
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Package suggested but not available for checking: ‘INLA’
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installed size is  5.8Mb
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installed size is 15.5Mb
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installed size is  7.7Mb
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installed size is  7.0Mb
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installed size is 136.7Mb
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installed size is 33.4Mb
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    libs   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 24.2Mb
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installed size is 15.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
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    libs  27.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  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
installed size is  8.8Mb
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    rda    7.0Mb
'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:
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    data   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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    threeBrainJS   2.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
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checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
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checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
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checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 84.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘ggplot2’
Package suggested but not available for checking: ‘lme4’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Package suggested but not available for checking: ‘SingleR’
installed size is 47.2Mb
  sub-directories of 1Mb or more:
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Running ‘testthat.R’ [13s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
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installed size is  6.4Mb
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Package suggested but not available for checking: ‘rrelaxiv’
installed size is 58.4Mb
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    tiledb  41.0Mb
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
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No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'org.Rn.eg.db', 'org.Mm.eg.db'
Found the following significant warnings:
  Warning: type_boxplot.Rd:35: unknown macro '\abbr'
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/tinyplot.Rcheck/00install.out’ for details.
prepare_Rd: type_boxplot.Rd:35: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
installed size is 97.5Mb
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    libs  94.2Mb
Specified C++14: please drop specification unless essential
installed size is  6.9Mb
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    data   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is 98.9Mb
  sub-directories of 1Mb or more:
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    libs  94.9Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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    libs   3.5Mb
'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
    libs   4.6Mb
Specified C++14: please drop specification unless essential
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    examples   5.0Mb
    include    3.6Mb
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
GNU make is a SystemRequirements.
'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
Specified C++11: please drop specification unless essential
installed size is 11.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
get_datasets: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stm’
Package unavailable to check Rd xrefs: ‘stm’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘gurobi’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is 203.3Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘toscaData’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.0Mb
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    data  13.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    doc    2.8Mb
Package suggested but not available for checking: ‘competitiontoolbox’
Package unavailable to check Rd xrefs: ‘competitiontoolbox’
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Package suggested but not available for checking: ‘taxidata’
installed size is 68.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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    libs   7.5Mb
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Package suggested but not available for checking: ‘ggtreeExtra’
Package suggested but not available for checking: ‘fwelnet’
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  8.7Mb
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    libs   3.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 10.4Mb
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installed size is  5.9Mb
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installed size is  8.4Mb
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    doc    3.1Mb
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installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘brms’
Package unavailable to check Rd xrefs: ‘brms’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
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    extdata  14.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 114.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 39.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/triptych.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Package unavailable to check Rd xrefs: ‘fpc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathabx.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {microtype}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is 44.9Mb
  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
installed size is 133.9Mb
  sub-directories of 1Mb or more:
    libs  132.7Mb
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 96.9Mb
  sub-directories of 1Mb or more:
    libs  95.9Mb
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
'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
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘twang’
'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:
    libs  19.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is 132.0Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs  128.8Mb
GNU make is a SystemRequirements.
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
Specified C++11: please drop specification unless essential
installed size is 27.2Mb
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    doc         1.4Mb
    dummydata   1.4Mb
    libs       22.6Mb
'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   5.3Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    help   4.4Mb
installed size is  5.4Mb
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    R      1.8Mb
    help   2.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'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  13.3Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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 66.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘adespatial’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  7.2Mb
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'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:
    R      2.6Mb
    data   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    doc   3.8Mb
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
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checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
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installed size is  7.4Mb
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    extdata   7.3Mb
installed size is  7.3Mb
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    data   7.1Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is 39.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  37.3Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'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 24.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
'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:
    libs   6.2Mb
installed size is 66.0Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs     61.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without 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  8.3Mb
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 15.2Mb
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    libs  15.2Mb
installed size is  7.9Mb
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    libs   7.6Mb
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
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    libs   7.9Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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installed size is  8.6Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘ggtern’
Specified C++11: please drop specification unless essential
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installed size is  5.2Mb
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    help   1.1Mb
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checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
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installed size is  9.6Mb
  sub-directories of 1Mb or more:
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    help   3.1Mb
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
Non-standard license specification:
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Standardizable: FALSE
installed size is  5.3Mb
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 55.7Mb
  sub-directories of 1Mb or more:
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    libs  54.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   5.3Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 33.0Mb
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GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 28.5Mb
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GNU make is a SystemRequirements.
installed size is 63.9Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'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:
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installed size is  9.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 117.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.8Mb
  sub-directories of 1Mb or more:
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    libs  10.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is 94.2Mb
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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
combine_filters : <anonymous>: no visible global function definition
  for ‘%||%’
Undefined global functions or variables:
  %||%
'LazyData' is specified without a 'data' directory
installed size is 58.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘classInt’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package suggested but not available for checking: ‘wordnetDicts’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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    libs   2.2Mb
'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:
    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:
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installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 44.0Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘wmtsa’
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Package suggested but not available for checking: ‘preprocessCore’
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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installed size is 14.8Mb
  sub-directories of 1Mb or more:
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installed size is 23.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 32.6Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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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
Package suggested but not available for checking: ‘nlmixr2’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.4Mb
installed size is 25.4Mb
  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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is 41.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 40.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
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    libs   4.6Mb
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'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 41.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  6.0Mb
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Package suggested but not available for checking: ‘rJava’
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/zoomerjoin.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘partitions’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.7Mb
  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
installed size is 13.6Mb
  sub-directories of 1Mb or more:
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Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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:
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checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  6.6Mb
  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
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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    data   2.9Mb
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installed size is  9.3Mb
  sub-directories of 1Mb or more:
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    doc      1.6Mb
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installed size is  9.4Mb
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'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:
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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
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'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'
Package which this enhances but not available for checking: 'asreml'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'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:
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    data   1.6Mb
    libs   1.0Mb
installed size is  7.1Mb
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    doc       3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
Specified C++11: please drop specification unless essential
'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 'ascariasis.Rmd' using rmarkdown
File figure/asc_plot_mixt-1.png not found in resource path
Error: processing vignette 'ascariasis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'ascariasis.Rmd'

--- re-building 'simulation_study.Rmd' using rmarkdown
File figure/sim_plot_true_data-1.png not found in resource path
Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'simulation_study.Rmd'

SUMMARY: processing the following files failed:
  'ascariasis.Rmd' 'simulation_study.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'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:
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Package required but not available: 'pwalign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
'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.
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
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    screenshots   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    data   2.1Mb
sort_asap: no visible global function definition for 'sort_by'
Undefined global functions or variables:
  sort_by
Package suggested but not available for checking: 'arcgisbinding'
Package suggested but not available for checking: 'ArchaeoData'
Found the following significant warnings:
  Warning: read_bcal.Rd:27: unknown macro '\abbr'
  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/ArchaeoPhases.Rcheck/00install.out' for details.
prepare_Rd: read_bcal.Rd:27: unknown macro '\abbr'
prepare_Rd: read_chronomodel.Rd:36: unknown macro '\abbr'
prepare_Rd: read_oxcal.Rd:27: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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    help   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 45.1Mb
  sub-directories of 1Mb or more:
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    libs  40.1Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'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:
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Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    libs   1.1Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    doc    4.0Mb
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    doc    3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
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
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   3.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
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installed size is  6.0Mb
  sub-directories of 1Mb or more:
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    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
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    help   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
'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'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
Package suggested but not available for checking: 'INLA'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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  6.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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:
    libs   6.0Mb
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
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.6Mb
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
installed size is 150.3Mb
  sub-directories of 1Mb or more:
    include  149.3Mb
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'INLA'
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    help   2.4Mb
    libs   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.0Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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.
Packages suggested but not available for checking: 'cmdstanr', 'blavsam'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.2Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   1.2Mb
'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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'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
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
    libs   1.2Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'brea.Rmd' using rmarkdown

Quitting from brea.Rmd:302-305 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `confint.glm()`:
! package 'MASS' must be installed
---
Backtrace:
    ▆
 1. ├─stats::confint(step_fit)
 2. └─stats:::confint.glm(step_fit)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'brea.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'brea.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   5.3Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.4Mb
    lib          5.0Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without 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:
    libs   3.2Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without 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 11.8Mb
  sub-directories of 1Mb or more:
    data   9.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'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  7.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    help      1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    entry_level                 1.7Mb
    virtual_patient_simulator   3.1Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
'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: 'rnaturalearthhires'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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/4.3/catlearn.Rcheck/00install.out' for details.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rkeops'
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
GNU make is a SystemRequirements.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc   16.4Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
--- re-building 'atp_calculation.Rmd' using rmarkdown
File mito_glyco_tests.png not found in resource path
Error: processing vignette 'atp_calculation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'atp_calculation.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Depends: includes the non-default packages:
  'coneproj', 'svDialogs', 'statmod', 'lme4', 'Matrix', 'splines2'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'chain_glm.Rmd' using rmarkdown

Quitting from chain_glm.Rmd:172-174 [glm1_3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `confint.glm()`:
! package 'MASS' must be installed
---
Backtrace:
    ▆
 1. ├─stats::confint(glm_res)
 2. └─stats:::confint.glm(glm_res)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'chain_glm.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'chain_glm.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R     5.0Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'darts'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'process_marker_data' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Package suggested but not available for checking: 'countreg'
'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'
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'README.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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  7.2Mb
  sub-directories of 1Mb or more:
    R         1.8Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'pwalign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is 48.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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    doc   6.5Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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Package suggested but not available for checking: 'monocle3'
Specified C++11: please drop specification unless essential
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checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
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installed size is  5.2Mb
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checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
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Package suggested but not available for checking: 'tobit1'
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GNU make is a SystemRequirements.
installed size is  5.2Mb
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Package suggested but not available for checking: 'PopGenome'
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.stop_not_number: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.6Mb
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    help   1.9Mb
installed size is  8.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is  6.0Mb
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    R      1.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
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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
installed size is  5.9Mb
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    extdata   2.4Mb
installed size is  5.1Mb
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    libs   2.8Mb
Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
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installed size is  7.0Mb
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Package suggested but not available for checking: 'CAM'
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checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  6.2Mb
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installed size is  5.3Mb
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GNU make is a SystemRequirements.
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installed size is  7.2Mb
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    vignette_data   2.6Mb
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
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installed size is  7.3Mb
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    R     2.1Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
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installed size is 18.0Mb
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installed size is  7.2Mb
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checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.0Mb
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installed size is  5.0Mb
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Specified C++11: please drop specification unless essential
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installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
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Package required and available but unsuitable version: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  8.4Mb
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    include   6.7Mb
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installed size is 24.9Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Problems with news in 'NEWS.md':
No news entries found.
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Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
installed size is  6.5Mb
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Package suggested but not available for checking: 'EnsDb.Hsapiens.v86'
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installed size is  5.8Mb
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Package suggested but not available for checking: 'INLA'
Running 'spelling.R' [0s]
  Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("crunchy")
  Loading required package: crunchy
  Loading required package: crunch
  
  Attaching package: 'crunch'
  
  The following objects are masked from 'package:stats':
  
      filter, rstandard, setNames
  
  The following object is masked from 'package:graphics':
  
      title
  
  The following object is masked from 'package:utils':
  
      write.csv
  
  The following object is masked from 'package:base':
  
      table
  
  Loading required package: shiny
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 28 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-gadgets.R:56:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-gadgets.R:69:5'): (code run outside of `test_that()`) ──────────
  Error: "test ds" not found
  Backtrace:
       ▆
    1. ├─global with_mock_crunch(...) at test-gadgets.R:63:1
    2. │ ├─base::with(opts, with_mock_api(expr))
    3. │ ├─crunch:::with.contextManager(opts, with_mock_api(expr))
    4. │ │ └─base::eval(substitute(expr), envir = parent.frame())
    5. │ │   └─base::eval(substitute(expr), envir = parent.frame())
    6. │ └─httptest::with_mock_api(expr)
    7. │   └─base::eval.parent(expr)
    8. │     └─base::eval(expr, p)
    9. └─crunch::loadDataset("test ds") at test-gadgets.R:69:5
   10.   └─httpcache::halt(dQuote(dataset), " not found")
  
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 28 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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    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  5.6Mb
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    data   3.8Mb
    doc    1.5Mb
installed size is  8.1Mb
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    doc   7.9Mb
installed size is  7.6Mb
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    data   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
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    R      1.2Mb
    data   1.7Mb
    libs   7.5Mb
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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
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installed size is  8.5Mb
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    libs   6.5Mb
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.
Packages required and available but unsuitable versions:
  'stats', 'tools', 'utils'

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
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'RGtk2'
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.3Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
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    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'CytOpt_HIPC.Rmd' using rmarkdown

Quitting from CytOpt_HIPC.Rmd:74-80 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! TypeError: float() argument must be a string or a number, not 'dict'
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─CytOpT::CytOpT(...)
 2.   └─pyCode$minMaxScale$Scale(X_s)
 3.     └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CytOpt_HIPC.Rmd' failed with diagnostics:
TypeError: float() argument must be a string or a number, not 'dict'
Run `reticulate::py_last_error()` for details.
--- failed re-building 'CytOpt_HIPC.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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Package which this enhances but not available for checking: 'doMC'
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installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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    data   4.4Mb
installed size is  7.6Mb
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    java   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    data   5.1Mb
LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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Package suggested but not available for checking: 'SASxport'
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installed size is  5.2Mb
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    libs   1.5Mb
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
Package suggested but not available for checking: 'INLA'
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
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    data   3.9Mb
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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installed size is  5.7Mb
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checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is  5.9Mb
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    doc    2.6Mb
    help   1.4Mb
    libs   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
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checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.9Mb
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    help   1.6Mb
    libs   1.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'signatureSearchData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 10.8Mb
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Package suggested but not available for checking: 'gurobi'
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
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installed size is 13.5Mb
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installed size is  5.0Mb
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    libs   4.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
installed size is  6.1Mb
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    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances 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
Running 'testthat.R' [95s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(distillML)
  > packageVersion("distillML")
  [1] '0.1.0.13'
  > 
  > test_check("distillML")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 83 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-predictor.R:57:3'): Tests that the predictor wrapper is working ──
  Error in ``[.data.frame`(wrapped_preds, , 1)`: undefined columns selected
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-predictor.R:57:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::all.equal(wrapped_preds[, 1], standard_preds, tolerance = 1e-04)
   5. ├─wrapped_preds[, 1]
   6. └─base::`[.data.frame`(wrapped_preds, , 1)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 83 ]
  Error: Test failures
  Execution halted
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without 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: 'BOLTSSIRR'
Running examples in 'divvy-Ex.R' failed
The error most likely occurred in:

> ### Name: rangeSize
> ### Title: Calculate common metrics of spatial distribution
> ### Aliases: rangeSize
> 
> ### ** Examples
> 
> # generate 20 occurrences for a pseudo-species
> # centred on Yellowstone National Park (latitude-longitude)
> # normally distributed with a standard deviation ~110 km
> set.seed(2)
> x <- rnorm(20, 110.5885, 2)
> y <- rnorm(20,  44.4280, 1)
> pts <- cbind(x,y)
> 
> rangeSize(pts)
Error in UseMethod("units") : 
  no applicable method for 'units' applied to an object of class "c('integer', 'numeric')"
Calls: rangeSize -> cbind -> cbind -> units
Execution halted
Error(s) in re-building vignettes:
--- re-building 'habitat-rangesize-case-study.Rmd' using rmarkdown
--- finished re-building 'habitat-rangesize-case-study.Rmd'

--- re-building 'subsampling-vignette.Rmd' using rmarkdown

Quitting from subsampling-vignette.Rmd:253-271 [meta data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'units' applied to an object of class "c('integer', 'numeric')"
---
Backtrace:
    ▆
 1. └─divvy::sdSumry(...)
 2.   └─divvy (local) dfsumry(dat)
 3.     └─divvy::rangeSize(coords = locs, crs = crs)
 4.       └─base::cbind(...)
 5.         └─units (local) cbind(deparse.level, ...)
 6.           └─base::units(dots[[1]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'subsampling-vignette.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "c('integer', 'numeric')"
--- failed re-building 'subsampling-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'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:
    include  15.8Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   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
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      2.0Mb
    extdata   2.3Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
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  5.3Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.2Mb
Package suggested but not available for checking: 'pwalign'
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checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
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checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
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checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.4Mb
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    data      1.7Mb
    extdata   3.2Mb
installed size is  5.6Mb
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    doc   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Running examples in 'dsem-Ex.R' failed
The error most likely occurred in:

> ### Name: dsemRTMB
> ### Title: Fit dynamic structural equation model
> ### Aliases: dsemRTMB
> 
> ### ** Examples
> 
> # Define model
> sem = "
+   # Link, lag, param_name
+   cprofits -> consumption, 0, a1
+   cprofits -> consumption, 1, a2
+   pwage -> consumption, 0, a3
+   gwage -> consumption, 0, a3
+   cprofits -> invest, 0, b1
+   cprofits -> invest, 1, b2
+   capital -> invest, 0, b3
+   gnp -> pwage, 0, c2
+   gnp -> pwage, 1, c3
+   time -> pwage, 0, c1
+ "
> 
> # Load data
> data(KleinI, package="AER")
> TS = ts(data.frame(KleinI, "time"=time(KleinI) - 1931))
> tsdata = TS[,c("time","gnp","pwage","cprofits",'consumption',
+                "gwage","invest","capital")]
> 
> # Fit model
> fit = dsemRTMB( sem=sem,
+             tsdata = tsdata,
+             estimate_delta0 = TRUE,
+             control = dsem_control(quiet=TRUE) )
Read 10 records
Error in advector(e1) : 
  Invalid argument to 'advector' (lost class attribute?)
Calls: dsemRTMB ... dgmrf -> as.vector -> Ops.advector -> Arith2 -> advector
Execution halted
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dsBase', 'dsBaseClient'
Packages suggested but not available for checking: 'dsBaseClient', 'dsBase'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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:
    htmlwidgets   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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    extdata   5.1Mb
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    data   7.3Mb
    doc    1.1Mb
Problems with news in 'NEWS.md':
No news entries found.
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Package suggested but not available for checking: 'lle'
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'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
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checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    doc    1.4Mb
installed size is  5.1Mb
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    data   3.9Mb
    libs   1.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
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    data   3.1Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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 'easycsv-Ex.R' failed
The error most likely occurred in:

> ### Name: fread_zip
> ### Title: read multiple csv files into named data frames
> ### Aliases: fread_zip
> ### Keywords: ~utilities ~misc
> 
> ### ** Examples
> 
> 
>   require(easycsv)
>   filezip <- system.file("exampleZips", "example_tables.zip", package="easycsv")
>   fread_zip(filezip)
Error in data.table::fread(input = tbl, sep = sep, nrows = nrows, header = header,  : 
  'autostart' is deprecated. Consider skip='string' or skip=n. This argument will be removed in the next release.
Calls: fread_zip -> <Anonymous> -> stopf -> raise_condition -> signal
Execution halted
'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'
'LazyData' is specified without 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 15.6Mb
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    doc    3.5Mb
    libs  11.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
The following files should probably not be installed:
  'econet.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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    help   2.7Mb
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
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Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.1Mb
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    libs   6.4Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'eHOF.Rnw' using knitr

Quitting from eHOF.Rnw:57-67 [4site.echo]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [germansl.infinitenature.org]: Connection time-out
---
Backtrace:
     x
  1. +-vegdata::tax("all")
  2. | \-vegdata:::load.taxlist(refl, detailed = detailed)
  3. |   +-httr::http_error(remote)
  4. |   \-httr:::http_error.character(remote)
  5. |     +-httr::http_error(HEAD(x, ...))
  6. |     \-httr::HEAD(x, ...)
  7. |       \-httr:::request_perform(req, hu$handle$handle)
  8. |         +-httr:::request_fetch(req$output, req$url, handle)
  9. |         \-httr:::request_fetch.write_memory(req$output, req$url, handle)
 10. |           \-curl::curl_fetch_memory(url, handle = handle)
 11. \-curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
Timeout was reached [germansl.infinitenature.org]: Connection time-out
--- failed re-building 'eHOF.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.4Mb
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    doc       5.1Mb
    extdata   5.1Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
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checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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installed size is  5.3Mb
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    libs   4.1Mb
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.3Mb
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Running examples in 'enmSdmX-Ex.R' failed
The error most likely occurred in:

> ### Name: coordImprecision
> ### Title: Calculate the precision of a geographic coordinate
> ### Aliases: coordImprecision
> 
> ### ** Examples
> 
> 
> # coarse-precision cases
> long <-	c(45, 45.1, 45.1)
> lat <-  c(45, 45.1, 45)
> ll <- cbind(long, lat)
> precision_m <- coordImprecision(ll)
> cbind(ll, precision_m)
Error in UseMethod("units") : 
  no applicable method for 'units' applied to an object of class "c('matrix', 'array', 'double', 'numeric')"
Calls: cbind -> cbind -> units
Execution halted
installed size is  7.3Mb
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    data   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (5) ePCR.Rd:0-17: Must have a \description
installed size is  5.6Mb
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    help   2.5Mb
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
installed size is 14.2Mb
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Package suggested but not available for checking: 'epidict'
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Package suggested but not available for checking: 'cmdstanr'
installed size is 10.6Mb
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Package unavailable to check Rd xrefs: 'cmdstanr'
GNU make is a SystemRequirements.
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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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc  13.3Mb
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
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installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
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No news entries found.
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checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
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    doc       1.6Mb
    extdata   2.4Mb
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'ExactData'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/excel.link.Rcheck/00install.out' for details.
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Package suggested but not available for checking: 'INLA'
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    app      2.7Mb
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'exuberdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'doMC'
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No news entries found.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    R      3.5Mb
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Problems with news in 'NEWS.md':
No news entries found.
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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    help   1.7Mb
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installed size is  5.8Mb
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    data   3.5Mb
    doc    1.0Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
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    Rcgi      3.0Mb
    cgi-bin   2.8Mb
.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  5.7Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/fdrDiscreteNull.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported object imported by a ':::' call: 'bit:::R_bit_as_hi'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'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:
    data   1.8Mb
    libs   1.2Mb
installed size is  6.1Mb
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    data   1.9Mb
    libs   2.3Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.1Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'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
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
search_finna : <anonymous>: no visible global function definition for
  '%||%'
search_finna : <anonymous> : <anonymous>: no visible global function
  definition for '%||%'
search_publisher : <anonymous>: no visible global function definition
  for '%||%'
Undefined global functions or variables:
  %||%
Running examples in 'finna-Ex.R' failed
The error most likely occurred in:

> ### Name: analyze_metadata
> ### Title: Analyze Refined Finna Metadata
> ### Aliases: analyze_metadata
> 
> ### ** Examples
> 
> library(finna)
> sibelius_data <- search_finna("sibelius")
Warning in search_finna("sibelius") :
  Default limit of 100 records is being used. Specify 'limit' argument for more records.
Error in record$id %||% NA : could not find function "%||%"
Calls: search_finna -> lapply -> FUN
Execution halted
Running 'testthat.R' [10s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(finna)
  > 
  > test_check("finna")
  Total results found: 2062442
  Data fetching completed in 2.71 seconds.
  Total results found: 3
  Data fetching completed in 0.24 seconds.
  Total results found: 2062442
  Data fetching completed in 2.05 seconds.
  No encoding supplied: defaulting to UTF-8.
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-search_publisher.R:3:3'): search_publisher performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_publisher("sibelius", limit = 10)) at test-search_publisher.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_publisher("sibelius", limit = 10)
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  ── Error ('test_search_finna.R:3:3'): search_finna performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_finna("sibelius", type = "Author")) at test_search_finna.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_finna("sibelius", type = "Author")
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown

Quitting from vignette.Rmd:22-26 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `record$id %||% NA`:
! could not find function "%||%"
---
Backtrace:
    ▆
 1. └─finna::search_finna("sibelius")
 2.   └─base::lapply(...)
 3.     └─finna (local) FUN(X[[i]], ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 14.2Mb
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    libs  12.8Mb
installed size is  5.5Mb
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    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    lib    3.0Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    doc   4.0Mb
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'gridlayout'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reliaR', 'STAR'
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Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
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    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
'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  21.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/flint.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    9.1Mb
    libs   1.0Mb
installed size is  7.1Mb
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    R   7.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    help   1.3Mb
installed size is  5.0Mb
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    htmlwidgets   3.9Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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  6.6Mb
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    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
Problems with news in 'NEWS.md':
No news entries found.
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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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without 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  6.5Mb
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    doc    1.1Mb
    help   1.0Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   2.7Mb
    libs   3.6Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Package suggested but not available for checking: 'dggrids'
installed size is 20.8Mb
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    doc    1.8Mb
    libs  13.0Mb
installed size is  5.2Mb
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    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'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
'LazyData' is specified without 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
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
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    doc    1.1Mb
    help   4.6Mb
Package suggested but not available for checking: 'EnsDb.Hsapiens.v75'
Error(s) in re-building vignettes:
--- re-building 'gaawr2.Rmd' using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo ${message} | \
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \
cat
rm hello.*"

Quitting from gaawr2.Rmd:407-413 [ensdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
---
Backtrace:
    ▆
 1. ├─ensembldb::metadata(EnsDb.Hsapiens.v75)
 2. └─base::.handleSimpleError(...)
 3.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building 'gaawr2.Rmd'

--- re-building 'web.Rmd' using rmarkdown
[WARNING] Citeproc: citation tsv not found
--- finished re-building 'web.Rmd'

SUMMARY: processing the following file failed:
  'gaawr2.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
install log '' does not exist
installed size is  8.6Mb
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    doc   7.4Mb
installed size is 33.6Mb
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    doc   31.8Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'paleofire'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 106.0Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     3.0Mb
    libs    91.0Mb
    proj     8.4Mb
installed size is 103.9Mb
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    extdata   1.3Mb
    gdal      3.0Mb
    libs     89.7Mb
    proj      8.4Mb
installed size is  5.8Mb
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    extdata   3.8Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
plot,GeDS-ANY: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
'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   3.2Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'pwalign'
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Error(s) in re-building vignettes:
--- re-building 'geoAr_geofacet.Rmd' using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_geofacet.Rmd'

--- re-building 'geoAr_leaflet.Rmd' using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_leaflet.Rmd'

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

SUMMARY: processing the following files failed:
  'geoAr_geofacet.Rmd' 'geoAr_leaflet.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:
    extdata   3.0Mb
    libs      1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    R        12.2Mb
    extdata   6.3Mb
    help      3.2Mb
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:
> cleanEx()
> nameEx("setMetadataStandard")
> ### * setMetadataStandard
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: setMetadataStandard
> ### Title: setMetadataStandard
> ### Aliases: setMetadataStandard
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  203.1 2.17 216.08 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 ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/GeoModels.Rcheck/00install.out' for details.
'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    1.2Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
Malformed Description field: should contain one or more complete sentences.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without 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       1.6Mb
    extdata   2.2Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   7.2Mb
'LazyData' is specified without a 'data' directory
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checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': 'scales:::censor'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'productplots:::bound'
  See the note in ?`:::` about the use of this operator.
'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
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    R      1.5Mb
    doc    2.3Mb
    help   1.1Mb
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Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
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    help       2.4Mb
    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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    Giac  18.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    help   3.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
Specified C++11: please drop specification unless essential
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.9Mb
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'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.
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs            4.4Mb
    test_data       2.3Mb
    vignette_data   2.1Mb
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
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checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
'LazyData' is specified without 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 47.5Mb
  sub-directories of 1Mb or more:
    i     45.3Mb
    libs   1.2Mb
'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  6.6Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'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
'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  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
jagam2greta: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
Package suggested but not available for checking: 'doMC'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    2.8Mb
    libs   1.0Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs                     1.3Mb
    supplementary_material   3.1Mb
Package required but not available: 'EnsDb.Hsapiens.v75'

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  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.1Mb
    help   1.8Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   8.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 267.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    help    1.0Mb
    java  264.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'hacksig.Rmd' using rmarkdown

Quitting from hacksig.Rmd:215-225 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `msigdbr()`:
! Unknown subcollection.
---
Backtrace:
    ▆
 1. ├─... %>% deframe()
 2. ├─tibble::deframe(.)
 3. ├─dplyr::mutate(., genes = map(genes, compose(as_vector, unname)))
 4. ├─tidyr::nest(., genes = c(gene_symbol))
 5. ├─dplyr::distinct(., gs_name, gene_symbol)
 6. └─msigdbr::msigdbr(species = "Homo sapiens", subcategory = "KEGG")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hacksig.Rmd' failed with diagnostics:
Unknown subcollection.
--- failed re-building 'hacksig.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
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
Package suggested but not available for checking: 'cmdstanr'
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package suggested but not available for checking: 'colorfulVennPlot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'hilldiv-Ex.R' failed
The error most likely occurred in:

> ### Name: div_profile_plot
> ### Title: Diversity profile plot
> ### Aliases: div_profile_plot
> ### Keywords: alpha beta gamma hill
> 
> ### ** Examples
> 
> data(bat.diet.otutable)
> data(bat.diet.hierarchy)
> #One sample example
> bat.diet.sample <- bat.diet.otutable[,1]
> profile.onesample <- div_profile(count=bat.diet.sample,qvalues=seq(from = 0, to = 5, by = (0.1)))
> div_profile_plot(profile.onesample)
> #Multiple samples
> profile.multiplesamples <- div_profile(bat.diet.otutable)
> div_profile_plot(profile.multiplesamples)
Error in melt.default(profile) : 
  The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both packages are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(profile). In the next version, this warning will become an error.
Calls: div_profile_plot ... melt -> melt.default -> stopf -> raise_condition -> signal
Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
Fdebug: multiple local function definitions for 'deb' with different
  formal arguments
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    4.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Package suggested but not available for checking: 'microViz'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
'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   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    help   1.1Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'hubExamples', 'hubVis'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
plotHVT: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'microViz'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.1Mb
'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
Package suggested but not available for checking: 'SparkR'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ICDS.Rcheck/00install.out' for details.
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:196:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:197:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:198:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/processthreadsapi.h:130:47: warning: ISO C does not allow extra ';' outside of a function [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:451:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1333:24: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1745:25: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winioctl.h:359:11: warning: ISO C forbids zero-size array 'SerialNumber' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/igraph.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.2Mb
    help   2.0Mb
    libs   6.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:447:19: warning: ISO C++ forbids flexible array member 'Format' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:548:37: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:499:29: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/imager.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     10.7Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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:
    data   3.3Mb
    doc    1.6Mb
    libs   1.0Mb
'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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
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'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
'LazyData' is specified without a 'data' directory
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
'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   5.2Mb
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.3Mb
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'iucnrdata'
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'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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'.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    help      2.0Mb
Package suggested but not available for checking: 'clonevol'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'remMap'
'LazyData' is specified without 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:
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kanjistat.data'
'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   9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   9.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
'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: 'rkward'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGeostats'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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: 'kadmin'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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:
  '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
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'using_latent2likert.Rmd' using rmarkdown
File man/figures/courses-grouped-min.png not found in resource path
Error: processing vignette 'using_latent2likert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'using_latent2likert.Rmd'

SUMMARY: processing the following file failed:
  'using_latent2likert.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without 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 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.8Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:196:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:197:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:198:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/processthreadsapi.h:130:47: warning: ISO C does not allow extra ';' outside of a function [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:451:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1333:24: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1745:25: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winioctl.h:359:11: warning: ISO C forbids zero-size array 'SerialNumber' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/leidenbase.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'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:
    help   1.1Mb
    libs   4.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rsyslog'
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'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          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R              1.4Mb
    doc-overview   2.2Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'EnsDb.Hsapiens.v75'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without 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: 'scio'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.0Mb
'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
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: 'kerdiest'
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without 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
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   1.1Mb
    libs   1.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/manifold.Rcheck/00install.out' for details.
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Problems with news in 'NEWS.md':
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    Bug Fixes
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Running examples in 'massiveGST-Ex.R' failed
The error most likely occurred in:

> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
ERROR: cannot open D:\temp\2025_03_21_01_50_00_4229\RtmpiOBt1v/WriteXLS/1.csv
. No such file or directory

Quitting from vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
    ▆
 1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
 2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
 3.   └─massiveGST:::plot.network(...)
 4.     ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
 5.     └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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Depends: includes the non-default packages:
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  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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    Bug Fix
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    Vignette
    Optimization
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  Warning: 'maximization_to_minimization' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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File ./man/figures/plot_peje.png not found in resource path
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SUMMARY: processing the following file failed:
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
Package suggested but not available for checking: 'fastshp'
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    5.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    CppCode   4.8Mb
    R         8.2Mb
    include  11.7Mb
    libs      1.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running examples in 'nJira-Ex.R' failed
The error most likely occurred in:

> ### Name: jira.query
> ### Title: Jira Query Interface
> ### Aliases: jira.query
> 
> ### ** Examples
> 
> issues <- jira.query(table = "issues", fields = "id AS IssueId, Created, Status, Priority", 
+ where = "project = 'HIVE' AND created >= '2019-01-01' AND created <= '2019-12-31' AND 
+ Status IN ('Open', 'Closed', 'Resolved')")
> 
> issues <- jira.query(table = "issues", fields = "id AS IssueId, Created", 
+ where = "'cf[10021]' = 'ABCD' AND Created > '2019-01-01'")
[1] "21-03-25 15:17:49 : Jira session inactive or expired. Sending login request"
[1] "21-03-25 15:17:50 : Jira Login Failed"
[1] "21-03-25 15:17:50 : jira: Error in Query"
[1] "21-03-25 15:17:50 : Field 'cf[10021]' does not exist or this field cannot be viewed by anonymous users."
> 
> history <- jira.query(table = "history", where = "id = 'HIVE-22692'")
[1] "21-03-25 15:17:50 : Jira session active."
> 
> history <- jira.query(table = "history", fields = "id AS IssueId, toString AS Status, 
+ COUNT(fromString) AS Count", where = "id = 'HIVE-22692' AND field = 'status'", 
+ groupby = "id,toString")
Error: Please install xml2 package
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'simpar'
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'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
'LazyData' is specified without 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  6.7Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
    mods   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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.0Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.1Mb
    libs   1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   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
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
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
'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: 'unix'
GNU make is a SystemRequirements.
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs   19.9Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.4Mb
    libs     5.1Mb
    models   4.8Mb
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  5.6Mb
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    doc   4.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   1.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
'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
Error(s) in re-building vignettes:
--- re-building 'OptimModel_vignette.Rmd' using rmarkdown

Quitting from OptimModel_vignette.Rmd:392-408 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `parse()`:
! <text>:11:1: unexpected '<'
10: attr(f.model,"srcref") <- 
11: <
    ^
---
Backtrace:
    ▆
 1. └─OptimModel::optim_fit(...)
 2.   ├─base::eval(parse(text = txt))
 3.   └─base::parse(text = txt)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'OptimModel_vignette.Rmd' failed with diagnostics:
<text>:11:1: unexpected '<'
10: attr(f.model,"srcref") <- 
11: <
    ^
--- failed re-building 'OptimModel_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
Package suggested but not available for checking: 'gurobi'
Problems with news in 'NEWS.md':
No news entries found.
'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   5.2Mb
    doc    1.8Mb
posterior_epred_ordbeta_prep: no visible global function definition for
  '%||%'
Undefined global functions or variables:
  %||%
Running examples in 'ordbetareg-Ex.R' failed
The error most likely occurred in:

> ### Name: posterior_epred_ordbeta.brmsfit
> ### Title: Calculate Probability of Response Components
> ### Aliases: posterior_epred_ordbeta.brmsfit posterior_epred_ordbeta
> 
> ### ** Examples
> 
> 
> data('ord_fit_mean')
> 
> # use function to calculate probability of top end of scale
> 
> pr_1s <- posterior_epred_ordbeta(ord_fit_mean,component="top")
Error in incl_thres %||% FALSE : could not find function "%||%"
Calls: posterior_epred_ordbeta ... posterior_epred_ordbeta.brmsfit -> posterior_epred_ordbeta_prep -> as_one_logical
Execution halted
Error(s) in re-building vignettes:
--- re-building 'package_introduction.qmd' using html


processing file: package_introduction.qmd
Error in incl_thres %||% FALSE : could not find function "%||%"
Calls: .main ... posterior_epred_ordbeta.brmsfit -> posterior_epred_ordbeta_prep -> as_one_logical

Quitting from package_introduction.qmd:287-297 [posterior_epred_ordbeta]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `incl_thres %||% FALSE`:
! could not find function "%||%"
---
Backtrace:
    ▆
 1. ├─... %>% hist
 2. ├─graphics::hist(.)
 3. ├─ordbetareg::posterior_epred_ordbeta(ord_fit_mean, component = "top")
 4. └─ordbetareg:::posterior_epred_ordbeta.brmsfit(ord_fit_mean, component = "top")
 5.   └─ordbetareg:::posterior_epred_ordbeta_prep(...)
 6.     └─ordbetareg:::as_one_logical(incl_thres %||% FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
Error: processing vignette 'package_introduction.qmd' failed with diagnostics:
✖ Error running quarto cli.
Caused by error:
! System command 'quarto.exe' failed
--- failed re-building 'package_introduction.qmd'

SUMMARY: processing the following file failed:
  'package_introduction.qmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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    R       1.0Mb
    nifti   3.8Mb
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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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.1Mb
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Package suggested but not available for checking: 'Rcplex'
Specified C++11: please drop specification unless essential
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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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   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 15.2Mb
  sub-directories of 1Mb or more:
    library  14.3Mb
Package suggested but not available for checking: 'CorShrink'
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'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
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checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   1.5Mb
Package required and available but unsuitable version: 'ggkegg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      7.8Mb
    help   2.8Mb
installed size is  6.8Mb
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    R      3.3Mb
    help   3.4Mb
installed size is  6.3Mb
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    R      3.1Mb
    help   3.0Mb
installed size is  6.6Mb
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    R      2.8Mb
    help   3.6Mb
installed size is  6.9Mb
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    R      3.1Mb
    help   3.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.3Mb
'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   2.7Mb
    doc    1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package suggested but not available for checking: 'PythonInR'
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs    7.4Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
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checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
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Package suggested but not available for checking: 'DMwR'
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checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
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    libs      1.8Mb
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.3Mb
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    doc    1.4Mb
    libs   1.3Mb
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'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
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GNU make is a SystemRequirements.
installed size is  5.6Mb
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    doc    2.1Mb
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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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
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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
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installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'pmartRdata'
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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
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Package unavailable to check Rd xrefs: 'INLA'
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checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
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checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'pollimetrydata'
Running examples in 'pollimetry-Ex.R' failed
The error most likely occurred in:

> ### Name: bodysize
> ### Title: Converts the intertegular distance (IT) and co-variates to body
> ###   size in dry weight (mg) for bees or hoverflies.
> ### Aliases: bodysize
> 
> ### ** Examples
> 
> example=cbind.data.frame(IT=c(1.3,2.3),
+                          Sex=c("Female","Male"), 
+                          Subfamily=c("Syrphinae","Eristalinae"),
+                          Region=c("Australasia","Europe"),
+                          Species=c("Sphaerophoria_macrogaster","Myathropa_florea"))
> bodysize(x=example,taxa="hov",type="taxo")
Loading required namespace: pollimetrydata
Failed with error:  'there is no package called 'pollimetrydata''
Downloading data from: https://github.com/liamkendall/pollimetrydata/raw/master/data/hov_tax_mod.rdata 

SHA-1 hash of the downloaded data file is:
8fabe989dfed6c91d8e5834ad224ff4865b76b7f
Loading required package: rstan
Loading required package: StanHeaders
Error: package or namespace load failed for 'rstan' in .doLoadActions(where, attach):
 error in load action .__A__.1 for package rstan: Rcpp::loadModule(module = "class_model_base", what = TRUE, env = ns, : Unable to load module "class_model_base": attempt to apply non-function
Error in .requirePackage(package) : 
  unable to find required package 'rstan'
Calls: bodysize ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
installed size is 12.2Mb
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installed size is  5.9Mb
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    libs   1.0Mb
installed size is  5.6Mb
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    libs      1.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  6.6Mb
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installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.5Mb
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'EnsDb.Hsapiens.v75'
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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
installed size is 10.0Mb
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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
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Package suggested but not available for checking: 'INLA'
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'cmdstanr'
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Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is  6.1Mb
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Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is  9.7Mb
  sub-directories of 1Mb or more:
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    libs   1.7Mb
Packages suggested but not available for checking: 'cmdstanr', 'iwmm'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'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
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
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installed size is 15.0Mb
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Packages suggested but not available for checking: 'unix', 'cmdstanr'
installed size is 23.6Mb
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installed size is  8.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cin'
Package suggested but not available for checking: 'rdt'
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Package suggested but not available for checking: 'rdt'
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installed size is 16.0Mb
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installed size is  6.3Mb
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installed size is  9.2Mb
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    libs   8.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.3Mb
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    doc   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/psp.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  7.8Mb
  sub-directories of 1Mb or more:
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    examples   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
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.6Mb
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installed size is 26.5Mb
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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
installed size is  5.9Mb
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Package suggested but not available for checking: 'spDataLarge'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
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GNU make is a SystemRequirements.
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
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    libs      2.9Mb
installed size is  5.1Mb
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installed size is 10.2Mb
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    contrib   3.7Mb
    doc       2.9Mb
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installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'fastshp'
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installed size is  5.2Mb
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    shiny_app   1.2Mb
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Package suggested but not available for checking: 'ReGenesees'
Warning: package needs dependence on R (>= 2.10)
GNU make is a SystemRequirements.
installed size is  5.0Mb
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Package suggested but not available for checking: 'bootmlm'
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.
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.
Package suggested but not available for checking: 'BRugs'
Unknown package 'BRugs' in Rd xrefs
installed size is 11.5Mb
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installed size is  7.3Mb
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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
installed size is 10.6Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.6Mb
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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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
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
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installed size is 11.6Mb
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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
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
No news entries found.
Running examples in 'randquotes-Ex.R' failed
The error most likely occurred in:

> ### Name: randquote
> ### Title: Get Random Quotes
> ### Aliases: randquote
> 
> ### ** Examples
> 
> randquote()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve hostname [quotesondesign.com]: Could not resolve host: quotesondesign.com
Calls: randquote ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
'LazyData' is specified without a 'data' directory
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installed size is  8.1Mb
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    extdata   4.1Mb
    libs      1.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
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    etc    1.9Mb
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checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
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installed size is  7.7Mb
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installed size is  5.1Mb
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    libs   1.3Mb
installed size is  5.3Mb
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
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Package suggested but not available for checking: 'rrelaxiv'
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installed size is  5.1Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
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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
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
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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  8.8Mb
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installed size is  7.5Mb
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Package suggested but not available for checking: 'pd.hg.u133.plus.2'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
installed size is  8.7Mb
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installed size is 39.8Mb
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Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 47.6Mb
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Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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    libs      1.2Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
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GNU make is a SystemRequirements.
installed size is 10.5Mb
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installed size is 13.4Mb
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installed size is 10.3Mb
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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
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
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installed size is  6.5Mb
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Package suggested but not available for checking: 'dataui'
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.3Mb
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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.
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    redengine  16.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.1Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
'LazyData' is specified without 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    3.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'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.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Package suggested but not available for checking: 'resourcecodedata'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/restfulr.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without 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/4.3/Rfast2.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   4.8Mb
    help   1.1Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
'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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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 13.8Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs    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
'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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
    libs      1.0Mb
'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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Riemann.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/RiemBase.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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    '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 nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 nor [v]sprintf. 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.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'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:
    include   3.4Mb
    libs      3.6Mb
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 50.2Mb
  sub-directories of 1Mb or more:
    R     4.1Mb
    exe  45.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
Error(s) in re-building vignettes:
--- re-building 'RLescalation.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'RLescalation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'RLescalation.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
GNU make is a SystemRequirements.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include   7.4Mb
    lib       3.0Mb
    libs      5.7Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rnaturalearthhires'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'bridgestan'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'rnaCrosslinkOO.Rmd' using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'rnaCrosslinkOO.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
'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   2.0Mb
    libs      3.3Mb
'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   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\emmintrin.h:134:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.7Mb
    libs   1.7Mb
Package suggested but not available for checking: 'RandomFields'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rpoppler.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'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   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Error(s) in re-building vignettes:
--- re-building 'benchmarks.Rmd' using rmarkdown
--- finished re-building 'benchmarks.Rmd'

--- re-building 'research_workflows.Rmd' using rmarkdown
File figure/unnamed-chunk-7-1.png not found in resource path
Error: processing vignette 'research_workflows.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'research_workflows.Rmd'

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

SUMMARY: processing the following file failed:
  'research_workflows.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
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   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  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_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 nor [v]sprintf. 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.
'LazyData' is specified without 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'
Specified C++11: please drop specification unless essential
'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  5.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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 18.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  11.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    1.9Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
Specified C++11: please drop specification unless essential
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/rswipl.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.0Mb
GNU make is a SystemRequirements.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Specified C++11: please drop specification unless essential
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rTorch)
  > 
  > test_check("rTorch")
  Error in !trace_length(trace) : invalid argument type
  Calls: test_check ... withCallingHandlers -> eval -> eval -> import -> py_module_import
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
Specified C++11: please drop specification unless essential
installed size is 11.3Mb
  sub-directories of 1Mb or more:
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    libs   2.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   9.8Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  'nimble' 'nimbleAPT'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
  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
Package which this enhances but not available for checking: 'glmmADMB'
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      5.3Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rWCVPdata'
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    include   1.1Mb
    libs      4.8Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'unix'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  8.4Mb
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checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 15.4Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'LazyData' is specified without 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
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   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
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
  sub-directories of 1Mb or more:
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    libs      2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    extdata  16.7Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'library' or 'require' call not declared from: 'tinyVAST'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/secrdesign.Rcheck/00install.out' for details.
'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      1.6Mb
    libs   2.1Mb
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
Malformed Title field: should not end in a period.
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 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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    models   1.6Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pwalign'
GNU make is a SystemRequirements.
'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    1.2Mb
    libs   3.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BPCells'
Packages suggested but not available for checking: 'BPCells', 'presto'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 107.6Mb
  sub-directories of 1Mb or more:
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    gdal     3.0Mb
    libs    89.8Mb
    proj     8.4Mb
    sqlite   1.5Mb
Specified C++11: please drop specification unless essential
'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:
  > library(testthat)
  > library(sgat)
  > 
  > test_check("sgat")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-initialization_sgat.R:1:1', 'test-sgat.R:1:1',
    'test-sgat_day.R:1:1', 'test-tripadvisor_places.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-ushuaia_restaurants.R:3:3'): gives vector ────────────────────
  length(restaurants) is not strictly more than 100. Difference: -25
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
'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:
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    libs   1.4Mb
Package suggested but not available for checking: 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
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'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:
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'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
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'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
'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:
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'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:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www  10.1Mb
'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
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
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    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/SIGN.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Error(s) in re-building vignettes:
--- re-building 'sim.BA.Rmd' using rmarkdown
File images/dag.png not found in resource path
Error: processing vignette 'sim.BA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sim.BA.Rmd'

SUMMARY: processing the following file failed:
  'sim.BA.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
'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.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Specified C++14: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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    libs   1.8Mb
Specified C++11: please drop specification unless essential
'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
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sjtable2df)
  > 
  > test_check("sjtable2df")
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  [ FAIL 1 | WARN 5 | SKIP 5 | PASS 18 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-mtab2df.R:48:5', 'test-mtab2df.R:136:5',
    'test-xtab2df.R:36:5', 'test-xtab2df.R:206:5', 'test-xtab2df.R:253:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mtab2df.R:134:5'): correct functioning of mtab2df: glmer ─────
  nrow(final_tab) == 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 5 | SKIP 5 | PASS 18 ]
  Error: Test failures
  Execution halted
Package which this enhances but not available for checking: 'kmndirs'
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
'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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without 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
Found the following significant warnings:

  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'doMC'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.4Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'lseq'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'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   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
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Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    doc    1.0Mb
Package suggested but not available for checking: 'gridlayout'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
    libs      1.1Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
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    libs      5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    libs   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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'SparseM.ontology':
  'as.matrix.csr' 'is.matrix.csr' 'is.matrix.csc' 'is.matrix.ssr'
  'is.matrix.ssc' 'is.matrix.coo'

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
installed size is 13.5Mb
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    libs  12.8Mb
'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 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.1Mb
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', '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.univar',
  '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.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.univar', '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.univar', '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  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.6Mb
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    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    help   1.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
    etc   2.1Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.8Mb
    doc    1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/spNetwork.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'user-guide.Rmd' using rmarkdown

Quitting from user-guide.Rmd:272-279 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'units' applied to an object of class "NULL"
---
Backtrace:
    ▆
 1. └─spqdep::Q.test(formula = f1, data = provinces_spain, m = 3, r = 1)
 2.   └─spqdep::m.surround(...)
 3.     └─base::rbind(mdtms, rowds)
 4.       └─units (local) rbind(deparse.level, ...)
 5.         └─base::units(dots[[1]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building 'user-guide.Rmd'

SUMMARY: processing the following file failed:
  'user-guide.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.0Mb
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    doc   5.5Mb
installed size is  5.0Mb
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    doc    1.5Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   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 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'starsdata'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
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))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    joss_paper   1.2Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
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    libs   9.3Mb
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
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    libs  34.5Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
'LazyData' is specified without 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'
installed size is  6.6Mb
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    data   2.0Mb
    doc    3.1Mb
    help   1.0Mb
installed size is  5.4Mb
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    libs   1.6Mb
Package suggested but not available for checking: 'velocyto.R'
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Package suggested but not available for checking: 'extraTrees'
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    tinytest   4.1Mb
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'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  6.5Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    2.5Mb
Package suggested but not available for checking: 'gurobi'
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    5.3Mb
Specified C++11: please drop specification unless essential
'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  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    dist3   2.0Mb
    dist4   1.7Mb
    dist5   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'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  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Error(s) in re-building vignettes:
--- re-building 'odesystem.Rmd' using rmarkdown

Quitting from odesystem.Rmd:76-83 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `Rcpp::sourceCpp()`:
! Error 1 occurred building shared library.
---
Backtrace:
    ▆
 1. └─symengine::ODESystem(lorenz_sys, method = "rk5_i")
 2.   └─Rcpp::sourceCpp(code = rcpp_code, env = compile_sys_env, verbose = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'odesystem.Rmd' failed with diagnostics:
Error 1 occurred building shared library.
--- failed re-building 'odesystem.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'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   2.9Mb
    doc    1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
installed size is  5.2Mb
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    R         1.3Mb
    extdata   3.1Mb
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
'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   5.9Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    8.2Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'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
installed size is  6.9Mb
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    doc   5.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    help   2.7Mb
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installed size is 108.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    gdal   3.0Mb
    libs  92.9Mb
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installed size is 23.3Mb
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    doc        1.1Mb
    libs       8.1Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/TestGenerator.Rcheck/00install.out' for details.
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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
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    data   1.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    R      4.1Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
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    R              1.2Mb
    threeBrainJS   2.9Mb
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checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
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checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
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checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
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checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
Error(s) in re-building vignettes:
--- re-building 'creating_prompt_wraps.Rmd' using rmarkdown
--- finished re-building 'creating_prompt_wraps.Rmd'

--- re-building 'getting_started.Rmd' using rmarkdown
File ../man/figures/answer_using_r1-1.png not found in resource path
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'getting_started.Rmd'

--- re-building 'sentiment_analysis.Rmd' using rmarkdown
File ../man/figures/plot_sentiment_analysis-1.png not found in resource path
Error: processing vignette 'sentiment_analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sentiment_analysis.Rmd'

SUMMARY: processing the following files failed:
  'getting_started.Rmd' 'sentiment_analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: type_boxplot.Rd:35: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/tinyplot.Rcheck/00install.out' for details.
prepare_Rd: type_boxplot.Rd:35: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.7Mb
Specified C++14: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    examples  12.7Mb
    include    3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.9Mb
'LazyData' is specified without a 'data' directory
get_datasets: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: 'gurobi'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/topologyGSA.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    R         5.9Mb
    help      1.7Mb
    include   1.9Mb
    libs     18.3Mb
Package suggested but not available for checking: 'toscaData'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  13.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'fwelnet', 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'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
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'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
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   2.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/unigd.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without 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 18.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.3Mb
    libs  14.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   7.3Mb
Unexported objects imported by ':::' calls:
  'usmapdata:::alaska_bbox' 'usmapdata:::ea_crs'
  'usmapdata:::hawaii_bbox' 'usmapdata:::transform_alaska'
  'usmapdata:::transform_hawaii'
  See the note in ?`:::` about the use of this operator.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'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  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 104.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     88.9Mb
    proj      8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without 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
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/vctrs.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
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    help   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    help   1.3Mb
'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
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     19.9Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'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   8.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   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
combine_filters : <anonymous>: no visible global function definition
  for '%||%'
Undefined global functions or variables:
  %||%
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'WindCurves_Info.Rmd' using rmarkdown

Quitting from WindCurves_Info.Rmd:65-77 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `source()`:
! dumpdata.R:2:1: unexpected '<'
1: random <-
2: <
   ^
---
Backtrace:
    ▆
 1. └─WindCurves::fitcurve(...)
 2.   ├─base::eval(dnew)
 3.   │ └─base::eval(dnew)
 4.   └─base::source("dumpdata.R")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'WindCurves_Info.Rmd' failed with diagnostics:
dumpdata.R:2:1: unexpected '<'
1: random <-
2: <
   ^
--- failed re-building 'WindCurves_Info.Rmd'

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

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

Quitting from winfapReader.Rmd:179-186 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `plot.window()`:
! need finite 'xlim' values
---
Backtrace:
     ▆
  1. └─base::sapply(...)
  2.   └─base::lapply(X = X, FUN = FUN, ...)
  3.     └─global FUN(X[[i]], ...)
  4.       ├─base::with(...)
  5.       └─base::with.default(...)
  6.         └─base::eval(substitute(expr), data, enclos = parent.frame())
  7.           └─base::eval(substitute(expr), data, enclos = parent.frame())
  8.             ├─base::plot(...)
  9.             └─graphics::plot.default(...)
 10.               └─graphics (local) localWindow(xlim, ylim, log, asp, ...)
 11.                 └─graphics::plot.window(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'winfapReader.Rmd' failed with diagnostics:
need finite 'xlim' values
--- failed re-building 'winfapReader.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'wordnetDicts'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
'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  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Package suggested but not available for checking: 'wmtsa'
Malformed Title field: should not end in a period.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.6Mb
'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   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    java  26.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'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
Found the following significant warnings:
  DocParse.c:1334:5: warning: 'xmlKeepBlanksDefault' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'Xplortext-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.LexChar
> ### Title: Plot LexChar objects
> ### Aliases: plot.LexChar
> ### Keywords: plot
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), var.agg="Gen_Edu", Fmin=10, Dmin=10,
+         remov.number=TRUE, stop.word.tm=TRUE)
> LD<-LexChar(res.TD,maxCharDoc = 0)
> plot(LD)
Error in `gtable_add_grob()`:
! `grobs` must be a single grob or a list of grobs, not a list.
Backtrace:
     ▆
  1. ├─base::plot(LD)
  2. └─Xplortext:::plot.LexChar(LD)
  3.   ├─base::suppressWarnings(...)
  4.   │ └─base::withCallingHandlers(...)
  5.   └─Xplortext (local) marrangeGrob2(grobs = pword, nrow = numr, ncol = numc, top = top)
  6.     ├─base::do.call(gridExtra::arrangeGrob, c(grobs[groups[[g]]], params))
  7.     └─gridExtra (local) `<fn>`(...)
  8.       └─gtable::gtable_add_grob(grobs = grobs)
  9.         └─gtable:::stop_input_type(grobs, "a single grob or a list of grobs")
 10.           └─rlang::abort(message, ..., call = call, arg = arg)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.4Mb
'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.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'a01_introduction.Rmd' using rmarkdown
--- finished re-building 'a01_introduction.Rmd'

--- re-building 'a02_workflow-tidycensus.Rmd' using rmarkdown

Quitting from a02_workflow-tidycensus.Rmd:28-35 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Failure when receiving data from the peer [api.census.gov]: Recv failure: Connection was reset
---
Backtrace:
     ▆
  1. ├─tidycensus::get_acs(...)
  2. │ ├─base::suppressWarnings(...)
  3. │ │ └─base::withCallingHandlers(...)
  4. │ └─tidycensus:::load_data_acs(...)
  5. │   └─httr::GET(...)
  6. │     └─httr:::request_perform(req, hu$handle$handle)
  7. │       ├─httr:::request_fetch(req$output, req$url, handle)
  8. │       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
  9. │         └─curl::curl_fetch_memory(url, handle = handle)
 10. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'a02_workflow-tidycensus.Rmd' failed with diagnostics:
Failure when receiving data from the peer [api.census.gov]: Recv failure: Connection was reset
--- failed re-building 'a02_workflow-tidycensus.Rmd'

--- re-building 'a03_developer-notes.Rmd' using rmarkdown
--- finished re-building 'a03_developer-notes.Rmd'

SUMMARY: processing the following file failed:
  'a02_workflow-tidycensus.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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory