GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/RSiena.Rcheck/00install.out’ for details.
Note: found 467 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.2Mb
    help   1.4Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 177.2Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.8Mb
    libs  170.1Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
GNU make is a SystemRequirements.
installed size is 256.4Mb
  sub-directories of 1Mb or more:
    lib    28.7Mb
    libs  225.0Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Note: found 117 marked UTF-8 strings
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Namespaces in Imports field not imported from:
  ‘bitops’ ‘httpuv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is 94.4Mb
  sub-directories of 1Mb or more:
    libs  94.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmarkdown   6.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs       2.1Mb
    projects   2.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Note: found 9 marked UTF-8 strings
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      3.4Mb
    extdata   1.4Mb
    libs      3.6Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘plyr’ ‘terra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.9Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  57.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘lubridate’ ‘rstantools’
  All declared Imports should be used.
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rjags’
Package unavailable to check Rd xrefs: ‘rjags’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
Package which this enhances but not available for checking: ‘glmmADMB’
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 65.0Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     59.6Mb
Found the following significant warnings:
  parser.cc:302:11: warning: 'daemon' is deprecated: first deprecated in macOS 10.5 - Use posix_spawn APIs instead. [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.2/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
    test   4.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Note: found 2016 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs    8.1Mb
    yacas   1.3Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs    8.8Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    libs  36.3Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 37 marked Latin-1 strings
  Note: found 172 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘saeHB’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Note: found 63 marked Latin-1 strings
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Note: found 120 marked UTF-8 strings
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  10.8Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  42.7Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.9Mb
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: ‘pcse’
‘sandwich-CL.Rnw’... [7s/7s] NOTE
differences from ‘sandwich-CL.Rout.save’
63,64c63,69
< Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'pcse'
---
> 
> Attaching package: 'pcse'
> 
> The following object is masked from 'package:sandwich':
> 
>     vcovPC
> 
165,166c170,171
< (Intercept) 0.022201 0.028359
< x           0.025276 0.028583
---
> (Intercept) 0.022201 0.022201
> x           0.025276 0.025276
176,177c181,182
< (Intercept)  0.022070 0.028359  0.022603 0.028359
< x            0.025338 0.028581  0.025241 0.028581
---
> (Intercept)  0.022070 0.022070  0.022603 0.022603
> x            0.025338 0.025338  0.025241 0.025241
  ‘sandwich-OOP.Rnw’... [2s/2s] OK
  ‘sandwich.Rnw’... [1s/1s] OK
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘FitARMA’
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.5Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.3Mb
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'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
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   3.2Mb
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘cowplot’ ‘easypackages’ ‘plyr’ ‘readr’ ‘stringr’
  ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocSingular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Nebulosa', 'infercnv'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘Matrix’ ‘SingleCellExperiment’ ‘SummarizedExperiment’
  ‘ggsci’
  All declared Imports should be used.
Package required but not available: ‘Synth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.5Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
Note: found 3 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  15.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rsbml’
Package required but not available: ‘ArrayExpress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.5Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs    20.8Mb
    models   1.6Mb
Note: found 836 marked UTF-8 strings
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
Note: found 3128 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘airway’
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
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    libs   7.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘geometries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 277.7Mb
  sub-directories of 1Mb or more:
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    libs    271.4Mb
    sqlite    1.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   4.9Mb
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘huge’
  All declared Imports should be used.
Package suggested but not available for checking: ‘hydromad’
Package suggested but not available for checking: ‘getCRUCLdata’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘scrypt’

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 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘scrypt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 2397 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  12.3Mb
Error(s) in re-building vignettes:
--- re-building ‘simmer-01-introduction.Rmd’ using rmarkdown
--- finished re-building ‘simmer-01-introduction.Rmd’

--- re-building ‘simmer-02-jss.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'simmer.plot'

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

    get_mon_arrivals, get_mon_attributes, get_mon_resources

Warning: Removed 16144 row(s) containing missing values (geom_path).
Warning: Removed 16144 row(s) containing missing values (geom_path).
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'simmer-02-jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/high-sierra-x86_64/results/4.2/simmer.Rcheck/vign_test/simmer/vignettes/simmer-02-jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See simmer-02-jss.log for more info.
--- failed re-building ‘simmer-02-jss.Rmd’

--- re-building ‘simmer-03-trajectories.Rmd’ using rmarkdown
--- finished re-building ‘simmer-03-trajectories.Rmd’

--- re-building ‘simmer-04-bank-1.Rmd’ using rmarkdown
--- finished re-building ‘simmer-04-bank-1.Rmd’

--- re-building ‘simmer-04-bank-2.Rmd’ using rmarkdown
--- finished re-building ‘simmer-04-bank-2.Rmd’

--- re-building ‘simmer-05-simpy.Rmd’ using rmarkdown
--- finished re-building ‘simmer-05-simpy.Rmd’

--- re-building ‘simmer-06-queueing.Rmd’ using rmarkdown
--- finished re-building ‘simmer-06-queueing.Rmd’

--- re-building ‘simmer-07-ctmc.Rmd’ using rmarkdown
--- finished re-building ‘simmer-07-ctmc.Rmd’

--- re-building ‘simmer-08-philosophers.Rmd’ using rmarkdown
--- finished re-building ‘simmer-08-philosophers.Rmd’

--- re-building ‘simmer-aa-5G.Rmd’ using rmarkdown
--- finished re-building ‘simmer-aa-5G.Rmd’

SUMMARY: processing the following file failed:
  ‘simmer-02-jss.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Package required but not available: ‘qpgraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rjags’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
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    libs  20.7Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    libs   2.8Mb
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.8Mb
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘CompQuadForm’ ‘boot’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Note: found 1122 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.4Mb
    libs   9.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
Packages suggested but not available for checking:
  'SNPlocs.Hsapiens.dbSNP144.GRCh38', 'MafDb.1Kgenomes.phase3.GRCh38',
  'BSgenome.Hsapiens.NCBI.GRCh38'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.9Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘itertools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘devtools’ ‘stats’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.1Mb
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘sos.Rnw’ using Sweave
Loading required package: brew

Attaching package: 'sos'

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

    ?

Warning in readLines(f) :
  incomplete final line found on '/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/cosso/INDEX'

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  13.0Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.2Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs  36.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Unknown package ‘sparsebn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘spatstat.core’ ‘spatstat.linnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.rmd’ using rmarkdown

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is 55.8Mb
  sub-directories of 1Mb or more:
    libs  54.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
Note: found 283 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘pheatmap’ ‘stats’ ‘viridis’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    help   2.8Mb
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Package unavailable to check Rd xrefs: ‘spatstat.model’
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Packages unavailable to check Rd xrefs: ‘spatstat.model’, ‘spatstat.explore’
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package suggested but not available for checking: ‘spatstat.model’
Package unavailable to check Rd xrefs: ‘spatstat.model’
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
Note: found 56 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
Note: found 34 marked UTF-8 strings
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Note: found 189 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘psy’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs     12.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7587 marked UTF-8 strings
Namespace in Imports field not imported from: ‘batchtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggridges’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  49.4Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’ ‘spatstat.linnet’ ‘spatstat.sparse’
  ‘spatstat.utils’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs  10.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  26.2Mb
'LazyData' is specified without a 'data' directory
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    libs  69.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gamboostLSS’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Note: found 40748 marked UTF-8 strings
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       1.8Mb
installed size is 69.0Mb
  sub-directories of 1Mb or more:
    libs  68.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pdftools’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xlsx’
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyselect’
  All declared Imports should be used.
Package suggested but not available for checking: ‘starsdata’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   1.7Mb
    nc    1.7Mb
Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> ### Name: st_warp
> ### Title: Warp (resample) grids in stars objects to a new grid, possibly
> ###   in an new coordinate reference system
> ### Aliases: st_warp
> 
> ### ** Examples
> 
> geomatrix = system.file("tif/geomatrix.tif", package = "stars")
> (x = read_stars(geomatrix))
stars object with 2 dimensions and 1 attribute
attribute(s):
               Min. 1st Qu. Median    Mean 3rd Qu. Max.
geomatrix.tif    74     107    123 126.765     132  255
dimension(s):
  from to  offset delta                refsys point values x/y
x    1 20 1841002   1.5 WGS 84 / UTM zone 11N  TRUE   NULL [x]
y    1 20 1144003  -1.5 WGS 84 / UTM zone 11N  TRUE   NULL [y]
sheared raster with parameters: -5 -5 
> new_crs = st_crs(4326)
> y = st_warp(x, crs = new_crs)
> plot(st_transform(st_as_sfc(st_bbox(x)), new_crs), col = NA, border = 'red')
> plot(st_as_sfc(y, as_points=FALSE), col = NA, border = 'green', axes = TRUE, add = TRUE)
> image(y, add = TRUE, nbreaks = 6)
> plot(st_as_sfc(y, as_points=TRUE), pch=3, cex=.5, col = 'blue', add = TRUE)
> plot(st_transform(st_as_sfc(x, as_points=FALSE), new_crs), add = TRUE)
> # warp 0-360 raster to -180-180 raster:
> r = read_stars(system.file("nc/reduced.nc", package = "stars"))
trying to read file: /Volumes/Builds/packages/high-sierra-x86_64/results/4.2/stars.Rcheck/stars/nc/reduced.nc
Error in CPL_read_gdal(as.character(x), as.character(options), as.character(driver),  : 
  file not found
Calls: read_stars ... is_big -> read_stars -> <Anonymous> -> CPL_read_gdal
Execution halted
Running ‘aggregate.R’ [2s/2s]
  Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4
< Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 8.2.1; sf_use_s2() is TRUE
---
> Linking to GEOS 3.10.2, GDAL 3.4.3, PROJ 8.2.0; sf_use_s2() is TRUE
  Running ‘align.R’ [2s/2s]
  Comparing ‘align.Rout’ to ‘align.Rout.save’ ... OK
  Running ‘area.R’ [1s/1s]
  Comparing ‘area.Rout’ to ‘area.Rout.save’ ... OK
  Running ‘crop.R’ [2s/2s]
  Comparing ‘crop.Rout’ to ‘crop.Rout.save’ ... OK
  Running ‘curvilinear.R’ [1s/1s]
  Comparing ‘curvilinear.Rout’ to ‘curvilinear.Rout.save’ ... OK
  Running ‘datasets.R’ [1s/1s]
  Comparing ‘datasets.Rout’ to ‘datasets.Rout.save’ ... OK
  Running ‘dimensions.R’ [1s/1s]
Running the tests in ‘tests/dimensions.R’ failed.
Complete output:
  > # https://github.com/r-spatial/stars/issues/295
  > suppressPackageStartupMessages(library(stars))
  > raw <- read_stars(system.file("nc/bcsd_obs_1999.nc", package = "stars"))
  trying to read file: /Volumes/Builds/packages/high-sierra-x86_64/results/4.2/stars.Rcheck/stars/nc/bcsd_obs_1999.nc
  Error in CPL_read_gdal(as.character(x), as.character(options), as.character(driver),  : 
    file not found
  Calls: read_stars ... is_big -> read_stars -> <Anonymous> -> CPL_read_gdal
  Execution halted
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 18 marked UTF-8 strings
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.3Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.1Mb
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Note: found 52 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Package required but not available: ‘pvca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MTS’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.7Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 1725 marked UTF-8 strings
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.3Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Note: found 83 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc  12.7Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mixtools’ ‘parallel’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.3Mb
    libs   1.6Mb
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Package suggested but not available for checking: ‘INLA’
installed size is 103.2Mb
  sub-directories of 1Mb or more:
    libs  102.3Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggtree’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.4Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Note: found 25 marked UTF-8 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   6.6Mb
DNF: multiple local function definitions for ‘mu_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘mu_y’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_y’ with different
  formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_x’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_y’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_x’
  with different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_y’
  with different formal arguments
modelSim: multiple local function definitions for ‘mu_x’ with different
  formal arguments
modelSim: multiple local function definitions for ‘mu_y’ with different
  formal arguments
modelSim: multiple local function definitions for ‘sigma_x’ with
  different formal arguments
modelSim: multiple local function definitions for ‘sigma_y’ with
  different formal arguments
'LazyData' is specified without a 'data' directory
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    libs  49.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘swephRdata’
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    fonts   1.7Mb
    libs   16.0Mb
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 81 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked Latin-1 strings
  Note: found 1270 marked UTF-8 strings
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 137 marked UTF-8 strings
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dearseq’
Package unavailable to check Rd xrefs: ‘dearseq’
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    libs  40.4Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    apps   2.3Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      2.0Mb
    telemac   1.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is 304.4Mb
  sub-directories of 1Mb or more:
    R       1.9Mb
    libs  301.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.8Mb
    tessdata  14.1Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
Note: found 3 marked UTF-8 strings
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.0Mb
    libs   4.1Mb
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Note: found 3 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘textreadr’
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc           1.6Mb
    htmlwidgets   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    libs  47.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'runjags', 'rjags', 'jagsUI'
Packages unavailable to check Rd xrefs: ‘runjags’, ‘rjags’, ‘jagsUI’
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’ ‘tidybins’ ‘validata’
  All declared Imports should be used.
Note: found 4546 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   4.4Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘bartMachine’
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs    12.6Mb
    tiledb  24.8Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2750 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 49.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  45.5Mb
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘OpenStreetMap’
Package unavailable to check Rd xrefs: ‘OpenStreetMap’
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    3.5Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘torch’
  All declared Imports should be used.
Package suggested but not available for checking: ‘katex’
installed size is 177.5Mb
  sub-directories of 1Mb or more:
    R          5.2Mb
    help       1.6Mb
    include    1.5Mb
    libs     168.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
  Note: found 701 marked UTF-8 strings
Package suggested but not available for checking: ‘taxidata’
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
'LazyData' is specified without a 'data' directory
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  49.5Mb
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   2.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    libs       1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.0Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 100.7Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  95.8Mb
'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
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ez’ ‘forcats’ ‘ggplot2’
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MTS’
Package unavailable to check Rd xrefs: ‘MTS’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
installed size is 68.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs  65.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       23.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   4.3Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
'LazyData' is specified without a 'data' directory
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  42.8Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lavaan’ ‘lifecycle’ ‘patchwork’ ‘ragg’ ‘scales’ ‘simstandard’
  All declared Imports should be used.
Note: found 7872 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USAboundariesData’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
Note: found 1 marked UTF-8 string
Note: found 33 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  24.5Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 128 marked UTF-8 strings
Note: found 49 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   2.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Running ‘testthat.R’ [36s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      destfile = input.data$datapath)`: download from 'https://www.polyploids.org/sites/default/files/2022-04/tetra_QTLpoly_data.RData' failed
  Backtrace:
      ▆
   1. └─utils::download.file(...) at test-QTLpoly.R:14:4
  
  [ FAIL 1 | WARN 3 | SKIP 2 | PASS 89 ]
  Deleting unused snapshots:
  • tetra_example/effects-bar.svg
  • tetra_example/effects-circle.svg
  • tetra_example/effects-digenic.svg
  • tetra_example/linkage-map-draw-names.svg
  • tetra_example/plot-map-list.svg
  • tetra_example/qtl-plot.svg
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  55.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.0Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘colorspace’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 56.1Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
Note: found 4954 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 69.1Mb
  sub-directories of 1Mb or more:
    libs  67.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘ecospat’ ‘jsonlite’
  ‘leaflet.extras’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’ ‘sp’
  ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.3Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Running examples in ‘warbleR-Ex.R’ failed
The error most likely occurred in:

> ### Name: image_to_wave
> ### Title: Convert images into wave objects
> ### Aliases: image_to_wave
> 
> ### ** Examples
> 
> { 
+  ### create image with text to use in the spectrogram
+  # remove margins of plot
+  par(mar = rep(0, 4))
+  
+  # empty plot
+  plot(0, type='n',axes = FALSE, ann = FALSE, xlim = c(0, 1), ylim = c(0, 1))
+  
+  # text to include
+  text <- " warbleR "
+  
+  # add text
+  text(x = 0.5, y = 0.5, labels = text, cex = 11, font = 1)
+  
+  # save image in temporary directory
+  dev2bitmap(file.path(tempdir(), "temp-img.png"), type = "pngmono", res = 30)
+  
+  # read it 
+   wv <- image_to_wave(file = file.path(tempdir(), "temp-img.png"), plot = TRUE, flim = c(1, 12))
+ 
+  # output wave object
+  # wv
+   
+  ## plot it   
+  # reset margins
+  par(mar = c(5, 4, 4, 2) + 0.1)
+  
+  # plot spectrogram
+  # spectro(wave = wv, scale = FALSE, collevels = seq(-30, 0, 5),
+  # palette = reverse.terrain.colors, ovlp = 90, grid = FALSE, flim = c(2, 11))
+ }
Error in dev2bitmap(file.path(tempdir(), "temp-img.png"), type = "pngmono",  : 
  GhostScript was not found
Execution halted
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1668 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3984 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 6738 marked UTF-8 strings
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.4Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.5Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    bin   4.2Mb
    lib   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 47.1Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    java  24.4Mb
'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
Package suggested but not available for checking: ‘xlsx’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   4.6Mb
Package suggested but not available for checking: ‘RNRCS’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘XML’ ‘atom4R’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Package suggested but not available for checking: ‘SDMTools’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.9Mb
    pictures   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: '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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
as.data.frame.feem.Rd:11: condition must be plain text
cmf.Rd:16: condition must be plain text
feem.Rd:19: condition must be plain text
feemflame.Rd:55: condition must be plain text
feemife.Rd:78: condition must be plain text
feemindex.Rd:83: condition must be plain text
feemjackknife.Rd:78: condition must be plain text
feemparafac.Rd:82: condition must be plain text
feemscatter.Rd:36: condition must be plain text
feemsplithalf.Rd:43: condition must be plain text
marine.colours.Rd:46: condition must be plain text
whittaker2.Rd:45: condition must be plain text
'LazyData' is specified without 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' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(allhomes)
  > 
  > test_check("allhomes")
  [2022-11-01 16:30:23] Looking up division ID for suburb='Arboretrum, ACT'...
  [2022-11-01 16:30:23] URL: https://www.allhomes.com.au/svc/locality/searchallbyname?st=ACT&n=arboretrum
  [ FAIL 1 | WARN 14 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-extract_past_sales_data.R:20'): Valid search returns `data.frame`/`tibble` ──
  extract_past_sales_data(18009, 2020, quiet = TRUE) is not an S3 object
  
  [ FAIL 1 | WARN 14 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.3Mb
'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
'LazyData' is specified without 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:
    extdata   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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/4.2/armada.Rcheck/00install.out' for details.
'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:
    R      2.3Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs  32.6Mb
Package which this enhances but not available for checking: 'ARTP'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.0Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   11.8Mb
    misc   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 4.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

  Natural language support but running in an English locale

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

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

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
'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:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
'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:
    libs   4.6Mb
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   3.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
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
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
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.9Mb
GNU make is a SystemRequirements.
'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
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    help   1.1Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
installed size is 146.7Mb
  sub-directories of 1Mb or more:
    include  145.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import 'dbscan::as.dendrogram' by 'stats::as.dendrogram' when loading 'Biopeak'
See 'd:/Rcompile/CRANpkg/local/4.2/Biopeak.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BiSEp.Rcheck/00install.out' for details.
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
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BonEV.Rcheck/00install.out' for details.
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include   9.0Mb
    lib      29.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    help   1.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    fonts   3.1Mb
    lib     4.5Mb
GNU make is a SystemRequirements.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bsplus)
  > 
  > test_check("bsplus")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-shiny.R:10'): iconlink works ───────────────────────────────────
  Error in `.tag_validate(iconlink$children[[1]], name = "i", class = "fa fa-info-circle")`: class is: fasfa-circle-info, needs to include: fafa-info-circle
  Backtrace:
      ▆
   1. ├─testthat::expect_identical(...) at test-shiny.R:10:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─bsplus:::.tag_validate(iconlink$children[[1]], name = "i", class = "fa fa-info-circle")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.1Mb
'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  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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc        2.1Mb
    pictures   4.1Mb
'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   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'GAMBoost'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    duckdb   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.4Mb
    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
'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: 'alr3'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: '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'
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
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'userfriendlyscience'
'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   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  6.1Mb
  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
'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:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.0Mb
'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
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(commonsMath)
  > 
  > test_check("commonsMath")
  
  Searching the system for Java.
    Failure with rscala home directory.
    Failure with JAVACMD environment variable.
    Failure with JAVA_HOME environment variable.
    Success with PATH environment variable.
    ... querying Java specifics.
  
  Searching the system for Scala.
    Failure with rscala home directory.
    Failure with SCALACMD environment variable.
    Failure with SCALA_HOME environment variable.
    Failure with PATH environment variable.
    Success with rscala package directory.
    ... querying Scala specifics.
  
  Searching the system for SBT.
    Failure with rscala home directory.
    Failure with SBTCMD environment variable.
    Failure with SBT_HOME environment variable.
    Failure with PATH environment variable.
    Failure with rscala package directory.
    Failure with rscala temporary directory.
  
  
  Starting instance. ********************************
  Error in if (!is.na(bytes)) { : the condition has length > 1
  Calls: test_check ... lapply -> FUN -> eval -> eval -> scala -> getHeapMaximum
  In addition: Warning messages:
  1: In system2("wmic", c("/locale:ms_409", "OS", "get", "FreePhysicalMemory",  :
    running command '"wmic" /locale:ms_409 OS get FreePhysicalMemory /VALUE' had status 4112
  2: In getHeapMaximum(heap.maximum, sConfig$javaArchitecture == 32) :
    NAs introduced by coercion
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'commonsMath.Rmd' using rmarkdown
Quitting from lines 33-38 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'commonsMath.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'CAM'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'conosPanel', 'p2data'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cec2005benchmark'
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  stemmer.c:171:26: warning: pointer targets in passing argument 1 of 'strlen' differ in signedness [-Wpointer-sign]
See 'd:/Rcompile/CRANpkg/local/4.2/corpus.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    libs   5.9Mb
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
GNU make is a SystemRequirements.
'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    1.7Mb
    libs   3.7Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    demos         4.3Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances 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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    deps  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dblog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11816 (sockconn)
Execution halted
Package suggested but not available for checking: 'doMC'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BRugs'
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'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       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
Package suggested but not available for checking: 'Rdonlp2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.5Mb
    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
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 suggested but not available for checking: 'doMC'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11311 (sockconn)
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11311 (sockconn)
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
Package suggested but not available for checking: 'rrelaxiv'
'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 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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'
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
'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 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
'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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    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
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.6Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'OpenMPController'
'LazyData' is specified without 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:
    assets   2.9Mb
    doc      2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    tutorials   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
'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
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
Codoc mismatches from documentation object 'IQLearnFS_VHet-methods':
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    bin       3.5Mb
    extdata   1.7Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'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
'LazyData' is specified without 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 required and available but unsuitable version: 'biomod2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  report.c:1466:31: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 1 and 8 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.2/epanet2toolkit.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'epidict'
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    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  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    java   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(era)
  > 
  > test_check("era")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 117 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-examples.R:17'): this_year() is vectorised ───────────────────
  this_year(c("CE", "BP", "AM")) (`actual`) not equal to list(year_now, year_now_bp, year_now_am) (`expected`).
  
  `actual[[3]]`:   "5783"
  `expected[[3]]`: "5782"
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 117 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   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
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ExactData'
'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 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'exuberdata'
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'fame/R/windows/zzz.R':
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section 'Good practice' in '?.onAttach'.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.0Mb
    help   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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
  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
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Rcgi      3.1Mb
    cgi-bin   2.9Mb
.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
Package suggested but not available for checking: 'NNLM'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported objects imported by ':::' calls:
  'fdapace:::GCVLwls1D1' 'fdapace:::GetSmoothedMeanCurve'
  'fdapace:::HandleNumericsAndNAN' 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/fdrDiscreteNull.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/FGSG.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'MicrobeDS'
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       2.2Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.6Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.2Mb
'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 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    9.0Mb
    libs   1.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
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 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    data   2.8Mb
    doc    1.4Mb
    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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.6Mb
    libs  12.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'foba', 'rrlda'
'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
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
'LazyData' is specified without 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
  sub-directories of 1Mb or more:
    doc   9.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     2.2Mb
    libs    49.3Mb
    proj     8.7Mb
Running examples in 'gdata-Ex.R' failed
The error most likely occurred in:

> ### Name: read.xls
> ### Title: Read Excel files
> ### Aliases: read.xls xls2csv xls2tab xls2tsv xls2sep
> ### Keywords: file
> 
> ### ** Examples
> 
> 
>    # iris.xls is included in the gregmisc package for use as an example
>    xlsfile <- file.path(path.package('gdata'),'xls','iris.xls')
>    xlsfile
[1] "D:/RCompile/CRANpkg/lib/4.2/gdata/xls/iris.xls"
> 
>    iris <- read.xls(xlsfile) # defaults to csv format
Error in findPerl(perl, verbose = verbose) : 
  perl executable not found. Use perl= argument to specify the correct path.
Calls: read.xls -> xls2sep -> findPerl
Error in file.exists(tfn) : invalid 'file' argument
Calls: read.xls -> file.exists
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Warnings in file 'R/utils.R':
  unable to translate '<U+00E9>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+2019>' to native encoding
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    data      2.3Mb
    doc       1.7Mb
    extdata   1.1Mb
    libs      1.3Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ###   Decimal degrees.
> ### Aliases: sexagesimal
> 
> ### ** Examples
> 
> # Latitude
> g <- -33
> m <- 38
> s <- 30.123456
> value <- sexagesimal(g, m, s, digits = 4)
> print(value)
[1] -33.6417
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  21.02 0.88 21.89 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
'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.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       5.2Mb
    extdata   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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ggOceanMapsData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'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
GNU make is a SystemRequirements.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs           13.9Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cplexAPI'
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.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
  'taxstats', 'taxstats1516'
'LazyData' is specified without a 'data' directory
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.6Mb
GNU make is a SystemRequirements.
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
Malformed Description field: should contain one or more complete sentences.
'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
Found the following problems:
GWASinlps.Rd:164:1: Warning: trimming empty <h4>
'LazyData' is specified without 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 182.2Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    java  179.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    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
'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
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'synbreed'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
    libs      2.0Mb
':::' call which should be '::': 'ggplot2:::guide_axis'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
'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
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Package suggested but not available for checking: 'ROI.plugin.mosek'
'LazyData' is specified without a 'data' directory
'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
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
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
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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  6.2Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  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
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
'LazyData' is specified without 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: 'rggobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    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
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs      9.8Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
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
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'example_hmm.Rmd' using rmarkdown
Thanks for using {fHMM} version 1.0.3!
See https://loelschlaeger.de/fHMM for help.
Type 'citation("fHMM")' for citing this R package.

Attaching package: 'fHMM'

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

    npar


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 38-45 (example_hmm.Rmd) 
Error: processing vignette 'example_hmm.Rmd' failed with diagnostics:
Problem while computing `obs = c(NA, diff(log(Close), lag = 1) * 100)`.
Caused by error in `log()`:
! non-numeric argument to mathematical function
--- failed re-building 'example_hmm.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  11.7Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.5Mb
'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'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'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:
    art_profiles   1.5Mb
    libs           8.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    i18n   4.0Mb
'LazyData' is specified without a 'data' directory
Package which this enhances 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
'LazyData' is specified without 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: multiple methods tables found for 'bootstrap'
  Warning: replacing previous import 'arkhe::bootstrap' by 'dimensio::bootstrap' when loading 'kairos'
See 'd:/Rcompile/CRANpkg/local/4.2/kairos.Rcheck/00install.out' for details.
Warning: multiple methods tables found for 'bootstrap'

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

Probably some imports need to be declared in the NAMESPACE file.
Running examples in 'kairos-Ex.R' failed
The error most likely occurred in:

> ### Name: fit
> ### Title: Frequency Increment Test
> ### Aliases: fit fit-method fit,data.frame,numeric-method
> ###   fit,matrix,numeric-method
> 
> ### ** Examples
> 
> data("merzbach", package = "folio")
> 
> ## Keep only decoration types that have a maximum frequency of at least 50
> keep <- apply(X = merzbach, MARGIN = 2, FUN = function(x) max(x) >= 50)
> counts <- merzbach[, keep]
> 
> ## Group by phase
> ## We use the row names as time coordinates (roman numerals)
> dates <- as.numeric(utils::as.roman(rownames(counts)))
> 
> ## Frequency Increment Test
> freq <- fit(counts, dates)
> 
> ## Plot time vs abundance and highlight selection
> plot(freq)
Warning: 'as_long()' is deprecated.
Use 'to_long()' instead.
See help("Deprecated")
Error: Must request at least one colour from a hue palette.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs             1.7Mb
    shiny-landsepi   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gof', 'lava.tobit'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.3Mb
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/liayson.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs       1.4Mb
    testdata   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rsyslog'
Package suggested but not available for checking: 'rsyslog'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Found the following significant warnings:
  lxb.c:62:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  lxb.c:62:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.2/lxb.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
GNU make is a SystemRequirements.
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(madrat)
  Loading required package: magclass
  > 
  > test_check("madrat")
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  • reshape2 cannot be loaded (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-config.R:3'): cache folder can be set properly ───────────────
  getwd() not identical to getConfig("cachefolder").
  1/1 mismatches
  x[1]: "d:/Rcompile/CRANpkg/local/4.2/madrat.Rcheck/tests/testthat"
  y[1]: "D:/RCompile/CRANpkg/local/4.2/madrat.Rcheck/tests/testthat"
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 386 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs  35.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
'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'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs          3.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scrubr'
'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:
    examples   2.7Mb
    libs       1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'flashr'
'LazyData' is specified without 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:
    java   3.3Mb
    libs   1.7Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
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:
gradient close to zero (gradtol) 
5  iterations
estimate: 1.940473 
Function value: -33.70681 
> vcov(a)
           [,1]
[1,] 0.03764041
> ## Estimate with analytic gradient and hessian
> a <- maxLik(loglik, gradlik, hesslik, start=1)
> vcov(a)
           [,1]
[1,] 0.03765436
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  6.25 0.13 6.46 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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: 'cplexAPI'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
'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   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    R     1.3Mb
    doc   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'genuMet'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.4Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'structSSI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'microcontax.data'
Package unavailable to check Rd xrefs: 'microcontax.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    5.5Mb
    lib    1.3Mb
    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  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
INFO - This is Biber 2.16
INFO - Logfile is 'README.blg'
INFO - Reading 'README.bcf'
ERROR - Error: Found biblatex control file version 3.9, expected version 3.7.
This means that your biber (2.16) and biblatex (3.18b) versions are incompatible.
See compat matrix in biblatex or biber PDF documentation.
INFO - ERRORS: 1
Warning: LaTeX Warning: Empty bibliography on input line 181.
Warning: LaTeX Warning: There were undefined references.
Warning: LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
Warning: Package rerunfilecheck Warning: File `README.out' has changed.
Warning: (rerunfilecheck)                Rerun to get outlines right
Warning: (rerunfilecheck)                or use package `bookmark'.
Warning: Package biblatex Warning: Please (re)run Biber on the file:
Warning: (biblatex)                README
Warning: (biblatex)                and rerun LaTeX afterwards.
Error: processing vignette 'README.Rmd' failed with diagnostics:
Failed to build the bibliography via biber
--- failed re-building 'README.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
'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:
    libs  13.2Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Flury'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'MoBPSmaps'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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 'Basic_Usage.Rmd' using rmarkdown
--- finished re-building 'Basic_Usage.Rmd'

--- re-building 'Comparison_Usage.Rmd' using rmarkdown
Quitting from lines 302-315 (Comparison_Usage.Rmd) 
Error: processing vignette 'Comparison_Usage.Rmd' failed with diagnostics:
'parameterFrequency' is not an exported object from 'namespace:irace'
--- failed re-building 'Comparison_Usage.Rmd'

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

--- re-building 'problem-definition.Rmd' using rmarkdown
--- finished re-building 'problem-definition.Rmd'

--- re-building 'writing-functions-for-moeadr.Rmd' using rmarkdown
--- finished re-building 'writing-functions-for-moeadr.Rmd'

SUMMARY: processing the following file failed:
  'Comparison_Usage.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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mortyr)
  > 
  > test_check("mortyr")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_returned_data.R:1'): (code run outside of `test_that()`) ───────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [rickandmortyapi.com] Resolving timed out after 10000 milliseconds
  Backtrace:
      ▆
   1. └─mortyr::get_characters() at test_returned_data.R:1:0
   2.   └─httr::GET("https://rickandmortyapi.com/api/character")
   3.     └─httr:::request_perform(req, hu$handle$handle)
   4.       ├─httr:::request_fetch(req$output, req$url, handle)
   5.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   6.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'corpus.useR.2008.abstracts'
Running examples in 'mpathsenser-Ex.R' failed
The error most likely occurred in:

> ### Name: geocode_rev
> ### Title: Reverse geocoding with latitude and longitude
> ### Aliases: geocode_rev
> 
> ### ** Examples
> 
> # Frankfurt Airport
> geocode_rev(50.037936, 8.5599631)
Warning in open.connection(con, "rb") :
  URL 'https://nominatim.openstreetmap.org/reverse.php?lat=50.037936&lon=8.5599631&email=&zoom=18&format=jsonv2': status was 'Couldn't resolve host name'
Error in open.connection(con, "rb") : 
  cannot open the connection to 'https://nominatim.openstreetmap.org/reverse.php?lat=50.037936&lon=8.5599631&email=&zoom=18&format=jsonv2'
Calls: geocode_rev ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   4.5Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   6.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'asreml'
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.3Mb
    models   1.1Mb
Running examples in 'naptanr-Ex.R' failed
The error most likely occurred in:

> ### Name: call_naptan_region
> ### Title: Call the Naptan API for a partial or full region name. Returns a
> ###   data frame of Naptan data.
> ### Aliases: call_naptan_region
> 
> ### ** Examples
> 
> 
> #Return data for west yorkshire only 
> call_naptan_region("west yorkshire")
Returning data for area codes: 450 West Yorkshire
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [naptan.api.dft.gov.uk] Resolving timed out after 10000 milliseconds
Calls: call_naptan_region ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(naptanr)
  > 
  > test_check("naptanr")
  Returning data for area codes: 450 West Yorkshire
  Returning data for area codes: 220 East Riding of Yorkshire, 320 North Yorkshire, 370 South Yorkshire, 450 West Yorkshire
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testcall_naptan.R:4'): (code run outside of `test_that()`) ──────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Could not resolve host: naptan.api.dft.gov.uk
  Backtrace:
      ▆
   1. └─naptanr::call_naptan() at testcall_naptan.R:4:0
   2.   └─httr::GET(url)
   3.     └─httr:::request_perform(req, hu$handle$handle)
   4.       ├─httr:::request_fetch(req$output, req$url, handle)
   5.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   6.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spatialClust'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("nat.utils")
  Loading required package: nat.utils
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 73 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • touch only supported on unix platforms (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fsutils.r:79'): common_path works ────────────────────────────
  common_path(c("/a", "/b"), normalise = T) not equal to np("/").
  1/1 mismatches
  x[1]: "d:/"
  y[1]: "D:/"
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 73 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 're2r'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'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 suggested but not available for checking: 'fastshp'
'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:
    libs  13.1Mb
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   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
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    CppCode   1.7Mb
    R         6.2Mb
    include   5.8Mb
    libs      1.2Mb
installed size is  6.7Mb
  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.
Running examples in 'njgeo-Ex.R' failed
The error most likely occurred in:

> ### Name: geocode_address_candidates
> ### Title: Geocode an address and retrieve all candidates using the NJOGIS
> ###   ArcGIS REST API
> ### Aliases: geocode_address_candidates
> 
> ### ** Examples
> 
> geocode_address_candidates(address = "33 Livingston Ave", city = "New Brunswick")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [geo.nj.gov] Resolving timed out after 10000 milliseconds
Calls: geocode_address_candidates ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 41-45 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Timeout was reached: [www.nomisweb.co.uk] Resolving timed out after 10000 milliseconds
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  6.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs   1.6Mb
'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
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
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            1.5Mb
    test_files   4.2Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.0Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [19s]
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.
  > #
  > 
  > library(testthat)
  > library(odns)
  > 
  > test_check("odns")
  [ FAIL 1 | WARN 0 | SKIP 23 | PASS 30 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (23)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-get_data.R:24'): correct result returned using dummy httr::GET result ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.opendata.nhs.scot] Resolving timed out after 10000 milliseconds
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-get_data.R:24:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─digest::digest(...)
    5. │ └─base::serialize(object, connection = NULL, ascii = ascii, version = serializeVersion)
    6. └─odns::get_data(...)
    7.   └─odns::resource_metadata(resource)
    8.     └─httr::GET(query)
    9.       └─httr:::request_perform(req, hu$handle$handle)
   10.         ├─httr:::request_fetch(req$output, req$url, handle)
   11.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   12.           └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 23 | PASS 30 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'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
Error(s) in re-building vignettes:
--- re-building 'onemapsgapi_vignette.Rmd' using rmarkdown
Quitting from lines 35-36 (onemapsgapi_vignette.Rmd) 
Error: processing vignette 'onemapsgapi_vignette.Rmd' failed with diagnostics:
Timeout was reached: [developers.onemap.sg] Resolving timed out after 10000 milliseconds
--- failed re-building 'onemapsgapi_vignette.Rmd'

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

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

> ### Name: oa_random
> ### Title: oa_fetch but for a random query
> ### Aliases: oa_random
> 
> ### ** Examples
> 
> oa_random()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [api.openalex.org] Connection timed out after 10008 milliseconds
Calls: oa_random ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs   13.1Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    libs     4.8Mb
    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  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   1.3Mb
    libs      1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   1.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Rcplex'
'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
Running examples in 'owidR-Ex.R' failed
The error most likely occurred in:

> ### Name: owid_plot
> ### Title: Plot an owid dataset
> ### Aliases: owid_plot
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> human_rights <- owid("human-rights-scores")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [ourworldindata.org] Resolving timed out after 10000 milliseconds
Calls: owid ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    library  19.4Mb
Package which this enhances but not available for checking: 'CorShrink'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'palmid-Ex.R' failed
The error most likely occurred in:

> ### Name: SerratusConnect
> ### Title: SerratusConnect
> ### Aliases: SerratusConnect
> ### Keywords: Serratus Tantalus palmid sql
> 
> ### ** Examples
> 
> con <- SerratusConnect()
Error in postgresqlNewConnection(dbDriver(drv), ...) : 
  RPosgreSQL error: could not connect public_reader@serratus-aurora-20210406.cluster-ro-ccz9y6yshbls.us-east-1.rds.amazonaws.com:5432 on dbname "summary": could not translate host name "serratus-aurora-20210406.cluster-ro-ccz9y6yshbls.us-east-1.rds.amazonaws.com" to address: Unknown host
Calls: SerratusConnect ... <Anonymous> -> <Anonymous> -> postgresqlNewConnection
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'PS1_Cat.Rmd' using rmarkdown
Quitting from lines 30-32 (PS1_Cat.Rmd) 
Error: processing vignette 'PS1_Cat.Rmd' failed with diagnostics:
Timeout was reached: [mast.stsci.edu] Resolving timed out after 10000 milliseconds
--- failed re-building 'PS1_Cat.Rmd'

--- re-building 'PS1_Images.Rmd' using rmarkdown
--- finished re-building 'PS1_Images.Rmd'

SUMMARY: processing the following file failed:
  'PS1_Cat.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  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
'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   2.7Mb
    doc    1.1Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  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
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   7.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Package suggested but not available for checking: 'PythonInR'
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs    6.9Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   2.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11976 (sockconn)
	<-CRANWIN2.fb05.statistik.uni-dortmund.de:11976 (sockconn)
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'DMwR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dendextendRcpp'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.2Mb
'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       1.5Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   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: '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
'LazyData' is specified without 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: 'ggsubplot'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [87s]
  Running 'wipe.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pkgload)
  > 
  > # Needed so that install.packages works correctly
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("pkgload")
  [ FAIL 4 | WARN 0 | SKIP 15 | PASS 338 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • "pkgload" %in% dev_packages() is not TRUE (1)
  • On CRAN (14)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-help.R:84'): shim_help and shim_questions works if topic moves ──
  rel_rd_path(shim_help("foofoo")) (`actual`) not equal to "foofoo.Rd" (`expected`).
  
  actual vs expected
  - "../../../../../../../../../RCompile/CRANpkg/local/4.2/pkgload.Rcheck/tests/testthat/testHelp/man/foofoo.Rd"
  + "foofoo.Rd"
  ── Failure ('test-help.R:85'): shim_help and shim_questions works if topic moves ──
  rel_rd_path(shim_question("foofoo")) (`actual`) not equal to "foofoo.Rd" (`expected`).
  
  actual vs expected
  - "../../../../../../../../../RCompile/CRANpkg/local/4.2/pkgload.Rcheck/tests/testthat/testHelp/man/foofoo.Rd"
  + "foofoo.Rd"
  ── Failure ('test-help.R:93'): shim_help and shim_questions works if topic moves ──
  rel_rd_path(shim_help("foofoo")) (`actual`) not equal to "barbar.Rd" (`expected`).
  
  actual vs expected
  - "../../../../../../../../../RCompile/CRANpkg/local/4.2/pkgload.Rcheck/tests/testthat/testHelp/man/barbar.Rd"
  + "barbar.Rd"
  ── Failure ('test-help.R:94'): shim_help and shim_questions works if topic moves ──
  rel_rd_path(shim_question("foofoo")) (`actual`) not equal to "barbar.Rd" (`expected`).
  
  actual vs expected
  - "../../../../../../../../../RCompile/CRANpkg/local/4.2/pkgload.Rcheck/tests/testthat/testHelp/man/barbar.Rd"
  + "barbar.Rd"
  
  [ FAIL 4 | WARN 0 | SKIP 15 | PASS 338 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    bin   8.6Mb
    doc   1.3Mb
'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:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'monocle3', 'ProjecTILs', 'SeuratWrappers'
'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:
    tests   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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'
Package unavailable to check Rd xrefs: 'INLA'
'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: 'pollimetrydata'
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Package suggested but not available for checking: 'WhopGenome'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    shinyApp   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.4Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    4.6Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'SDMTools'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
Package suggested but not available for checking: 'rdt'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rdt'
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.5Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
    gui          1.6Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.0Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
Package suggested but not available for checking: 'RDCOMClient'
'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
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'
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 10.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  10.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    R   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'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
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'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
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
    po    2.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/Rcplex.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.2Mb
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    include  45.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/Rcpp.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    include        1.5Mb
    jsonexamples   3.8Mb
    libs           1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: Bad session key
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 18 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-decrypt.r:69'): Decryption with passphrase passthrough and armor works ──
  Error in `file(con, "r")`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::readLines("file2-decrypt.txt") at test-decrypt.r:69:2
   2.   └─base::file(con, "r")
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   1.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'dataui'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'Rediscover.Rmd' using rmarkdown
Loading required package: Matrix
Loading required package: speedglm
Loading required package: MASS
Loading required package: PoissonBinomial
Loading required package: ShiftConvolvePoibin
Loading required package: matrixStats

Attaching package: 'dplyr'

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

    count

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

    select

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'kableExtra'

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

    group_rows

Quitting from lines 21-30 (Rediscover.Rmd) 
Error: processing vignette 'Rediscover.Rmd' failed with diagnostics:
package or namespace load failed for 'TCGAbiolinks' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace 'TCGAbiolinksGUI.data' 1.12.0 is being loaded, but >= 1.15.1 is required
--- failed re-building 'Rediscover.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
    include   1.9Mb
    libs      1.6Mb
    models    1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   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
'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/4.2/rgdal.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
'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  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc     1.1Mb
    fonts   1.5Mb
    libs    2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
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
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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  8.1Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.2Mb
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_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
    libs      7.8Mb
'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:
    data   3.6Mb
    doc    1.5Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rinit.c:170:24: warning: pointer targets in passing argument 2 of 'Re_ReadConsole' differ in signedness [-Wpointer-sign]
  Rinit.c:251:21: warning: assignment to 'int (*)(const char *, unsigned char *, int,  int)' from incompatible pointer type 'int (*)(const char *, char *, int,  int)' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/rJava.Rcheck/00install.out' for details.
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/4.2/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. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'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:
    include   2.9Mb
    libs      2.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.9Mb
'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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
'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  9.0Mb
  sub-directories of 1Mb or more:
    rmd   8.0Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
'LazyData' is specified without a 'data' directory
Running examples in 'RMixtComp-Ex.R' failed
The error most likely occurred in:

> ### Name: RMixtComp-package
> ### Title: RMixtComp
> ### Aliases: RMixtComp-package
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> 
> data(simData)
>  
> # define the algorithm's parameters: you can use createAlgo function
> algo <- list(nbBurnInIter = 50,
+              nbIter = 50,
+              nbGibbsBurnInIter = 50,
+              nbGibbsIter = 50,
+              nInitPerClass = 20,
+              nSemTry = 20,
+              confidenceLevel = 0.95)
> 
> # run RMixtComp for learning using only 3 variables
> resLearn <- mixtCompLearn(simData$dataLearn$matrix, simData$model$unsupervised[1:3], algo,
+                           nClass = 1:2, nRun = 2, nCore = 1)
====== Run MixtComp in learn mode with 2 run(s) per number of classes and 1 core(s)
Data: 200 individuals and 3 variables.
-- K = 1
Start run 1 on thread number 83884
Run 1 DONE on thread number 83884
Start run 2 on thread number 83884
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
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 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'III_individual_phenometrics.Rmd' using knitr
--- finished re-building 'III_individual_phenometrics.Rmd'

--- re-building 'II_status_intensity.Rmd' using knitr
--- finished re-building 'II_status_intensity.Rmd'

--- re-building 'IV_site_phenometrics.Rmd' using knitr
--- finished re-building 'IV_site_phenometrics.Rmd'

--- re-building 'I_introduction.Rmd' using knitr
--- finished re-building 'I_introduction.Rmd'

--- re-building 'VIII_data_cleaning.Rmd' using knitr
--- finished re-building 'VIII_data_cleaning.Rmd'

--- re-building 'VII_combine_raster_point.Rmd' using knitr
--- finished re-building 'VII_combine_raster_point.Rmd'

--- re-building 'VI_geospatial.Rmd' using knitr
trying URL 'https://geoserver.usanpn.org/geoserver/wcs?service=WCS&version=2.0.1&request=GetCoverage&format=geotiff&coverageId=gdd:agdd_50f&SUBSET=time("2019-06-25T00:00:00.000Z")'
Quitting from lines 127-131 (VI_geospatial.Rmd) 
Error: processing vignette 'VI_geospatial.Rmd' failed with diagnostics:
need finite 'xlim' values
--- failed re-building 'VI_geospatial.Rmd'

--- re-building 'V_magnitude_phenometrics.Rmd' using knitr
--- finished re-building 'V_magnitude_phenometrics.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'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
'LazyData' is specified without 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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              2.2Mb
    simulationStudy   1.6Mb
'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
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
installed size is 37.0Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  35.6Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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/4.2/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
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   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'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
Running examples in 'r.proxy-Ex.R' failed
The error most likely occurred in:

> ### Name: noproxy
> ### Title: Reset proxy
> ### Aliases: noproxy
> 
> ### ** Examples
> 
> noproxy()
Proxy was cleaned!

check what your ip is: 
IPv4: 
129.217.207.166

Details: 
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html> <!--[if lt IE 7
                     (right here) ------^
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    dependencies  20.2Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if ( ! isTRUE(tryCatch({rscala::scalaConfig(reconfig="offline")}, error=function(e) TRUE)) ) {
  +   library(testthat)
  +   library(rscala)
  +   test_check("rscala")
  + }
  
  Searching the system for Java.
    Failure with rscala home directory.
    Failure with JAVACMD environment variable.
    Failure with JAVA_HOME environment variable.
    Success with PATH environment variable.
    ... querying Java specifics.
  
  Searching the system for Scala.
    Failure with rscala home directory.
    Failure with SCALACMD environment variable.
    Failure with SCALA_HOME environment variable.
    Failure with PATH environment variable.
    Success with rscala package directory.
    ... querying Scala specifics.
  
  Searching the system for SBT.
    Failure with rscala home directory.
    Failure with SBTCMD environment variable.
    Failure with SBT_HOME environment variable.
    Failure with PATH environment variable.
    Failure with rscala package directory.
    Failure with rscala temporary directory.
  
  
  Starting instance. ********************************
  Error in if (!is.na(bytes)) { : the condition has length > 1
  Calls: test_check ... lapply -> FUN -> eval -> eval -> scala -> getHeapMaximum
  In addition: Warning messages:
  1: In system2("wmic", c("/locale:ms_409", "OS", "get", "FreePhysicalMemory",  :
    running command '"wmic" /locale:ms_409 OS get FreePhysicalMemory /VALUE' had status 4112
  2: In getHeapMaximum(heap.maximum, sConfig$javaArchitecture == 32) :
    NAs introduced by coercion
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'rscala.Rnw' using knitr
Quitting from lines 277-280 (rscala.Rnw) 
Error: processing vignette 'rscala.Rnw' failed with diagnostics:
the condition has length > 1
--- failed re-building 'rscala.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/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. 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
'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  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.2Mb
    help   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.8Mb
    libs   8.9Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    lib    2.0Mb
    libs   5.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    rmarkdown   6.6Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      3.4Mb
    extdata   1.4Mb
    libs      1.3Mb
'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:
    doc    7.8Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Running examples in 'rtry-Ex.R' failed
The error most likely occurred in:

> ### Name: rtry_geocoding
> ### Title: Perform geocoding
> ### Aliases: rtry_geocoding
> 
> ### ** Examples
> 
> # Convert the address of MPI-BGC ("Hans-Knoell-Strasse 10, 07745 Jena, Germany")
> # into coordinates in latitudes and longitudes
> # Note: Please change to your own email address when executing this function
> rtry_geocoding("Hans-Knoell-Strasse 10, 07745 Jena, Germany",
+    email = "john.doe@example.com")
Warning in open.connection(con, "rb") :
  URL 'http://nominatim.openstreetmap.org/search/Hans-Knoell-Strasse%2010,%2007745%20Jena,%20Germany?format=json&addressdetails=0&limit=1&email=john.doe@example.com': status was 'Couldn't resolve host name'
Error in rtry_geocoding("Hans-Knoell-Strasse 10, 07745 Jena, Germany",  : 
  object 'geocode' not found
Execution halted
Package suggested but not available for checking: 'cmdstanr'
Unknown package 'cmdstanr' in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'glmmADMB'
'LazyData' is specified without a 'data' directory
'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 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'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
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
Package suggested but not available for checking: 'unix'
'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:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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   3.9Mb
    libs   1.2Mb
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'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:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
'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:
    R      1.5Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
Package which this enhances 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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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     3.3Mb
    models   1.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    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  6.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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/4.2/sf.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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hydromad'
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'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:
    R      2.1Mb
    libs   1.5Mb
'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
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rPython'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.4Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'MafDb.1Kgenomes.phase3.GRCh38'
'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:
    R     3.2Mb
    doc   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.1Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'spatialEco-Ex.R' failed
The error most likely occurred in:

> ### Name: cgls_urls
> ### Title: Provide URL's for Copernicus Global Land Service datasets
> ### Aliases: cgls_urls
> 
> ### ** Examples
> 
> # Create date string for query
> d <- seq(as.Date("2020/05/01"), as.Date("2020-09-01"), by="day")
> 
> # Search for 300m (333m) LAI within specified date range 
> all.urls <- cgls_urls(dates = d, resolution = 300, 
+                         product = "lai")		
Warning in readLines(manifest.url) :
  URL 'https://land.copernicus.vgt.vito.be/manifest/': status was 'Failure when receiving data from the peer'
Error in readLines(manifest.url) : cannot read from connection
Calls: cgls_urls -> paste -> readLines
Execution halted
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  13.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    help   2.8Mb
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Package unavailable to check Rd xrefs: 'spatstat.model'
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Packages unavailable to check Rd xrefs: 'spatstat.model', 'spatstat.explore'
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Packages unavailable to check Rd xrefs: 'spatstat.model', 'spatstat.explore'
Error(s) in re-building vignettes:
--- re-building 'bugfixes.Rnw' using Sweave
Loading required package: spatstat.data
Loading required package: spatstat.geom
spatstat.geom 3.0-3
Loading required package: spatstat.random
spatstat.random 2.2-0
Loading required package: spatstat.core
Loading required package: nlme
Loading required package: rpart
spatstat.core 2.4-4
Loading required package: spatstat.linnet
spatstat.linnet 2.3-2

spatstat 2.3-4       (nickname: 'Watch this space') 
For an introduction to spatstat, type 'beginner' 

--- finished re-building 'bugfixes.Rnw'

--- re-building 'datasets.Rnw' using Sweave
--- finished re-building 'datasets.Rnw'

--- re-building 'getstart.Rnw' using Sweave
--- finished re-building 'getstart.Rnw'

--- re-building 'replicated.Rnw' using Sweave
Loading required namespace: spatstat.explore
Failed with error:  'there is no package called 'spatstat.explore''

Error: processing vignette 'replicated.Rnw' failed with diagnostics:
 chunk 31 
Error : Package 'spatstat.explore' is required for plotting objects of class 'fv'

--- failed re-building 'replicated.Rnw'

--- re-building 'shapefiles.Rnw' using Sweave
--- finished re-building 'shapefiles.Rnw'

--- re-building 'updates.Rnw' using Sweave
--- finished re-building 'updates.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'spatstat.model'
Package unavailable to check Rd xrefs: 'spatstat.model'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  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 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  13.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   9.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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
Package suggested but not available for checking: 'starsdata'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   1.7Mb
    nc    1.7Mb
'LazyData' is specified without a 'data' directory
Running examples in 'statcanR-Ex.R' failed
The error most likely occurred in:

> ### Name: statcan_data
> ### Title: statcanR
> ### Aliases: statcan_data
> 
> ### ** Examples
> 
> mydata <- statcan_data('27-10-0014-01', 'eng')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www150.statcan.gc.ca] Resolving timed out after 10000 milliseconds
Calls: statcan_data ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
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))
'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:
    shiny-apps   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Running 'testthat.R' [172s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("stokes")
  Loading required package: stokes
  Loading required package: spray
  
  Attaching package: 'spray'
  
  The following objects are masked from 'package:base':
  
      pmax, pmin
  
  
  Attaching package: 'stokes'
  
  The following object is masked from 'package:spray':
  
      zap
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 977 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_transform.R:16'): Function pullback() behaves itself ─────────
  issmall(discrepancy) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  list(index = c(4, 1, 2, 5, 5, 5), value = c(0.499352699874198, -1.64182731678488, -1.70794186809151))
  c(0.858170048957342, 0.36589086563891, 0.676384873708268, 0.931527176605764, 0.851228600014032, -1.4741354019524, 0.919616569136682, 0.470803484807186, -0.86832358325045, -0.000428712074411446, -0.0399024121917049, 0.03207926148745, 0.275060985729183, -0.214530493378387, -0.751219801632788, 0.188890309533881, -1.97821109648701, -1.22644570518357, 0.716971852589262, -0.346015633015644, 0.543791913626087, 1.10169856540597, 1.42977372369748, 0.035356531481477, -0.517690378908219)
  Backtrace:
      ▆
   1. └─stokes (local) foo(o, M) at test_transform.R:16:8
   2.   └─testthat::expect_true(issmall(discrepancy), info = list(x, M)) at test_transform.R:10:8
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 977 ]
  Error: Test failures
  Execution halted
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: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Malformed Title field: should not end in a period.
'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
Found the following significant warnings:
  icu69/common/cstring.h:43:70: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 156 bytes from a string of length 156 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.2/stringi.Rcheck/00install.out' for details.
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
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
'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   2.0Mb
    doc    3.3Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc  12.7Mb
'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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.3Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'INLA'
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.4Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
DNF: multiple local function definitions for 'mu_x' with different
  formal arguments
DNF: multiple local function definitions for 'mu_y' with different
  formal arguments
DNF: multiple local function definitions for 'sigma_x' with different
  formal arguments
DNF: multiple local function definitions for 'sigma_y' with different
  formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'mu_x' with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'mu_y' with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'sigma_x'
  with different formal arguments
DNFOptim : MLE_f: multiple local function definitions for 'sigma_y'
  with different formal arguments
modelSim: multiple local function definitions for 'mu_x' with different
  formal arguments
modelSim: multiple local function definitions for 'mu_y' with different
  formal arguments
modelSim: multiple local function definitions for 'sigma_x' with
  different formal arguments
modelSim: multiple local function definitions for 'sigma_y' with
  different formal arguments
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
'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: 'cplexAPI'
Package suggested but not available for checking: 'cplexAPI'
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'dingemanse-data-example.Rmd' using rmarkdown
--- finished re-building 'dingemanse-data-example.Rmd'

--- re-building 'quick-start.Rmd' using rmarkdown
--- finished re-building 'quick-start.Rmd'

--- re-building 'synr-creategroup.Rmd' using rmarkdown
--- finished re-building 'synr-creategroup.Rmd'

--- re-building 'synr-tutorial.Rmd' using rmarkdown
--- finished re-building 'synr-tutorial.Rmd'

--- re-building 'validate-data.Rmd' using rmarkdown
Quitting from lines 295-327 (validate-data.Rmd) 
Error: processing vignette 'validate-data.Rmd' failed with diagnostics:
Timeout was reached: [] Resolving timed out after 10000 milliseconds
--- failed re-building 'validate-data.Rmd'

SUMMARY: processing the following file failed:
  'validate-data.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
Package suggested but not available for checking: 'unix'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: multiple methods tables found for 'bootstrap'
See 'd:/Rcompile/CRANpkg/local/4.2/tabula.Rcheck/00install.out' for details.
Missing link or links in documentation object 'reexports.Rd':
  '[arkhe:remove]{remove_empty}' '[arkhe:remove]{remove_NA}'
  '[arkhe:remove]{remove_zero}' '[arkhe:replace]{replace_NA}'
  '[arkhe:replace]{replace_zero}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following significant warnings:

  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' is deprecated.
  Warning: 'as_long()' 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 'bibliography.Rmd' using rmarkdown
--- finished re-building 'bibliography.Rmd'

--- re-building 'diversity.Rmd' using rmarkdown
Quitting from lines 355-358 (diversity.Rmd) 
Error: processing vignette 'diversity.Rmd' failed with diagnostics:
Continuous value supplied to discrete scale
--- failed re-building 'diversity.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tashudata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
Malformed Description field: should contain one or more complete sentences.
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  6.2Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      1.1Mb
    telemac   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  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/terra.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'bootstrap'
See 'd:/Rcompile/CRANpkg/local/4.2/tesselle.Rcheck/00install.out' for details.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       6.9Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'mnlogit'
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.0Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lmdb/mdb.c:10787:24: warning: ISO C does not support the 'I' printf flag [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.2/thor.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc           1.7Mb
    htmlwidgets   2.3Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   4.5Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    examples  12.6Mb
    include    3.5Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'corpus.JSS.papers'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    R         5.2Mb
    help      1.6Mb
    include   1.5Mb
    libs     16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.1Mb
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without 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: 'TreeDistData'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    libs       1.1Mb
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   7.1Mb
'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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    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
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
Package which this enhances but not available for checking: 'sl3'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   4.3Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  14.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'urltools-Ex.R' failed
The error most likely occurred in:

> ### Name: tld_extract
> ### Title: Extract TLDs
> ### Aliases: tld_extract
> 
> ### ** Examples
> 
> # Using the inbuilt dataset
> domains <- domain("https://en.wikipedia.org/wiki/Main_Page")
> tld_extract(domains)
            domain tld
1 en.wikipedia.org org
> 
> # Using a refreshed one
> tld_extract(domains, tld_refresh())
Warning in file(con, "r") :
  URL 'http://data.iana.org/TLD/tlds-alpha-by-domain.txt': status was 'Couldn't resolve host name'
Error in file(con, "r") : 
  cannot open the connection to 'http://data.iana.org/TLD/tlds-alpha-by-domain.txt'
Calls: tld_extract -> tld_refresh -> readLines -> file
Execution halted
Package suggested but not available for checking: 'USAboundariesData'
Package suggested but not available for checking: 'USA.state.boundaries.data'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
'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 17.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.3Mb
'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
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   2.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Could not fetch https://ignacio.martinez.fyi/vizdraws/prior.html
HttpExceptionRequest Request {
  host                 = "ignacio.martinez.fyi"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/vizdraws/prior.html"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "ignacio.martinez.fyi" [Network.Socket.connect: <socket: 792>: failed (Connection timed out (WSAETIMEDOUT))]))
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building 'introduction.Rmd'

--- re-building 'shiny-example.Rmd' using rmarkdown
--- finished re-building 'shiny-example.Rmd'

SUMMARY: processing the following file failed:
  'introduction.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
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    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  8.9Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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: 'prepr'
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
'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.
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
Found the following significant warnings:
  assp/asspfio.c:678:34: warning: ISO C does not support the 'I' printf flag [-Wformat=]
  assp/asspfio.c:684:33: warning: ISO C does not support the 'I' printf flag [-Wformat=]
  assp/asspfio.c:710:33: warning: ISO C does not support the 'I' printf flag [-Wformat=]
  assp/asspfio.c:716:33: warning: ISO C does not support the 'I' printf flag [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.2/wrassp.Rcheck/00install.out' for details.
Malformed Title field: should not end in a period.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    java  24.4Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(xpectr)
  > 
  > test_check("xpectr")
  [ FAIL 1 | WARN 5 | SKIP 2 | PASS 841 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • skipping due to breaking changes in R 4.0.0 (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_capture_side_effects.R:30'): capture_side_effects() works with tibbles ──
  strip(output_10856[["error"]]) %in% ... is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 5 | SKIP 2 | PASS 841 ]
  Error: Test failures
  Execution halted
'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:
    include   4.0Mb
    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
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
'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
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Package suggested but not available for checking: 'SDMTools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 96.4Mb
  sub-directories of 1Mb or more:
    libs  95.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.5Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Note: found 596 marked UTF-8 strings
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is 14.1Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking:
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installed size is  5.1Mb
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Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘patchwork’
  All declared Imports should be used.
Package required but not available: ‘BSgenome.Mmusculus.UCSC.mm10’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DeconRNASeq’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.3Mb
    files   1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    doc   2.8Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Namespaces in Imports field not imported from:
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  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rjags’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'R2jags', 'jagsUI'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without 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:
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installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
'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
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 231 marked UTF-8 strings
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 36.8Mb
  sub-directories of 1Mb or more:
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    libs    35.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GEOquery’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    R  36.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Running ‘testthat.R’ [20s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected` is a logical vector (TRUE)
  ── Failure ('test-prodStack.R:456'): prodStack must work with refStudy, if interactive is set to TRUE and if x is a list of antaresDataList and refStudy an antaresDataList ,  ──
  isTRUE(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-prodStack.R:470'): prodStack must work with refStudy, if interactive is set to TRUE and if x is a list of antaresDataList and refStudy an antaresDataList ,  ──
  all.equal(...) is not TRUE
  
  `actual` is a character vector ('Mean absolute difference: 2500')
  `expected` is a logical vector (TRUE)
  
  [ FAIL 12 | WARN 1 | SKIP 13 | PASS 290 ]
  Error: Test failures
  Execution halted
installed size is  7.0Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.3Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
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  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R             3.0Mb
    help          1.1Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package unavailable to check Rd xrefs: ‘GLAD’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 84.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs  78.4Mb
Note: found 1409 marked UTF-8 strings
Package which this enhances but not available for checking: ‘ARTP’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 899 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    java   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions:
  'parallel', 'stats', 'base'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.3Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
Error(s) in re-building vignettes:
  ...
--- re-building ‘baffle.Rmd’ using rmarkdown
Quitting from lines 88-95 (baffle.Rmd) 
Error: processing vignette 'baffle.Rmd' failed with diagnostics:
unused arguments (title.font = 2, title.cex = 1.5)
--- failed re-building ‘baffle.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 89.7Mb
  sub-directories of 1Mb or more:
    libs  87.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is 86.7Mb
  sub-directories of 1Mb or more:
    libs  85.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   1.3Mb
    doc    1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   4.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.9Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GO.db', 'GSEABase', 'org.Hs.eg.db', 'reactome.db'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
installed size is 90.5Mb
  sub-directories of 1Mb or more:
    libs  88.5Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  44.5Mb
Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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installed size is 114.2Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
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installed size is 102.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 96.7Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
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Package suggested but not available for checking: ‘PottsUtils’
installed size is  9.0Mb
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installed size is  8.8Mb
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GNU make is a SystemRequirements.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
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installed size is 17.3Mb
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Namespace in Imports field not imported from: ‘FastGP’
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installed size is 31.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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installed size is 11.1Mb
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Namespaces in Imports field not imported from:
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installed size is 13.4Mb
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Namespace in Imports field not imported from: ‘RcppNumerical’
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installed size is  8.4Mb
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installed size is  8.3Mb
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Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
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installed size is 86.3Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
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installed size is 16.9Mb
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installed size is  5.6Mb
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installed size is  5.7Mb
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Namespace in Imports field not imported from: ‘Rdpack’
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installed size is  6.6Mb
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Namespace in Imports field not imported from: ‘dplyr’
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installed size is 10.7Mb
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GNU make is a SystemRequirements.
installed size is 33.1Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
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'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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'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
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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Packages suggested but not available for checking: 'BRugs', 'rjags'
Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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installed size is 105.8Mb
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Namespace in Imports field not imported from: ‘rstantools’
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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installed size is  7.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 49.9Mb
  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 15.3Mb
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Namespace in Imports field not imported from: ‘forecast’
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'LazyData' is specified without a 'data' directory
installed size is 49.4Mb
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Namespace in Imports field not imported from: ‘rstantools’
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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 29.2Mb
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Namespace in Imports field not imported from: ‘BiDAG’
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Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
installed size is 63.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
'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  5.3Mb
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Note: found 10089 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 156.6Mb
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installed size is  6.5Mb
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'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘nycflights13’
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Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
installed size is  9.8Mb
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Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is  5.4Mb
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Note: found 940 marked Latin-1 strings
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
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Package suggested but not available for checking: ‘RODBC’
Package suggested but not available for checking: ‘RODBC’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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Checking should be performed on sources prepared by ‘R CMD build’.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
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Namespace in Imports field not imported from: ‘runonce’
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Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
installed size is 12.0Mb
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Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  7.5Mb
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installed size is 19.8Mb
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installed size is  5.1Mb
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Namespace in Imports field not imported from: ‘tibble’
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Note: found 660 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 92.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
Package required but not available: ‘MEIGOR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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installed size is  8.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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Note: found 46 marked UTF-8 strings
Package suggested but not available for checking: ‘rpanel’
Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Packages in Depends field not imported from:
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  These packages need to be imported from (in the NAMESPACE file)
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  7.0Mb
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Package suggested but not available for checking: ‘IHW’
installed size is 38.6Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 85.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  9.4Mb
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Namespace in Imports field not imported from: ‘RcppArmadillo’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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installed size is  6.7Mb
  sub-directories of 1Mb or more:
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'::' or ':::' import not declared from: ‘StochBlockTest’
'library' or 'require' call not declared from: ‘StochBlockTest’
installed size is 17.3Mb
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Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
installed size is 168.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 105.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 53.2Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 92.0Mb
  sub-directories of 1Mb or more:
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    libs  84.7Mb
GNU make is a SystemRequirements.
installed size is  8.3Mb
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Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 16.2Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘sangerseqR’
installed size is 362.8Mb
  sub-directories of 1Mb or more:
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    lib      353.6Mb
GNU make is a SystemRequirements.
installed size is 92.9Mb
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installed size is  7.2Mb
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Namespace in Imports field not imported from: ‘sna’
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Namespace in Imports field not imported from: ‘usethis’
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Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘qvalue’
Package unavailable to check Rd xrefs: ‘qvalue’
installed size is  5.4Mb
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GNU make is a SystemRequirements.
installed size is 90.0Mb
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Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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installed size is  6.0Mb
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installed size is  5.0Mb
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Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Note: found 2487 marked UTF-8 strings
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [49s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  as.numeric(b_lincom[, 5]) not equal to 0.0005428401.
  1/1 mismatches
  [1] 0.016 - 0.000543 == 0.0155
  ── Failure ('test-parametric_bootstrap.R:170'): p-value are at least approximately uniform under null (univariate mixed-effects model) ──
  max(abs(sapply(pvals, function(x) mean(pvals <= x)) - pvals)) not equal to 0.1.
  1/1 mismatches
  [1] 0.3 - 0.1 == 0.2
  ── Failure ('test-parametric_bootstrap.R:280'): simulate_betta_random does a reasonable thing ──
  mean(...) not equal to 1.02.
  1/1 mismatches
  [1] 0.961 - 1.02 == -0.0586
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 250 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 33.6Mb
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.4Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  8.1Mb
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Package suggested but not available for checking: ‘glmmADMB’
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installed size is  5.7Mb
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Namespaces in Imports field not imported from:
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installed size is  9.6Mb
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Namespace in Imports field not imported from: ‘DBI’
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 33.4Mb
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Namespaces in Imports field not imported from:
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installed size is 110.6Mb
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installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    libs  48.1Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qgraph’ ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is 59.6Mb
  sub-directories of 1Mb or more:
    libs  59.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Note: found 287 marked UTF-8 strings
Note: found 512 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Package suggested but not available for checking: ‘GenomicRanges’
Package unavailable to check Rd xrefs: ‘GenomicRanges’
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Note: found 1 marked UTF-8 string
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘reshape2’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs  27.0Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.4Mb
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.9Mb
'LazyData' is specified without a 'data' directory
installed size is 195.6Mb
  sub-directories of 1Mb or more:
    libs  195.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    duckdb   3.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
Namespace in Imports field not imported from: ‘urltools’
  All declared Imports should be used.
Note: found 907 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.4Mb
    libs  10.1Mb
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GLAD’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Package required but not available: ‘TxDb.Mmusculus.UCSC.mm10.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28982 marked UTF-8 strings
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.8Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RODBC’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘methods’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'GO.db', 'moe430a.db'
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 4622 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 30244 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/CohensdpLibrary.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘R6’ ‘formatR’ ‘jsonlite’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'pcalg', 'CAM'
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  29.7Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
installed size is 85.6Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RODBC’
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs          3.2Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
    libs      1.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Package suggested but not available for checking: ‘xcms’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.7Mb
Note: found 139613 marked UTF-8 strings
Package suggested but not available for checking: ‘rjags’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Package unavailable to check Rd xrefs: ‘rjags’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 1934235 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Note: found 2385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Note: found 20 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘qvalue’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked UTF-8 strings
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer2’
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 500 marked UTF-8 strings
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Note: found 282 marked UTF-8 strings
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
Note: found 3031 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 1350 marked UTF-8 strings
installed size is 151.1Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    data    1.6Mb
    libs  146.2Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package which this enhances 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  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    demos         4.3Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘fs’ ‘googleCloudStorageR’
  All declared Imports should be used.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    deps  10.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   4.5Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    libs  67.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
Package suggested but not available for checking: ‘msa’
Note: found 2596 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54315 marked UTF-8 strings
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.5Mb
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RedeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘bslib’ ‘knitr’ ‘matrixStats’ ‘rmarkdown’ ‘shinythemes’ ‘tidyverse’
  All declared Imports should be used.
Package required but not available: ‘dnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 62.7Mb
  sub-directories of 1Mb or more:
    libs  62.2Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   6.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 37.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  34.9Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
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    help   1.5Mb
    libs   3.1Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dclone', 'dcmle'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.8Mb
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.1Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘plyr’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    libs  66.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘IHW’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 8014 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘Actgram_diurnality_avg_activity.Rmd’ using rmarkdown
Quitting from lines 30-36 (Actgram_diurnality_avg_activity.Rmd) 
Error: processing vignette 'Actgram_diurnality_avg_activity.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Actgram_diurnality_avg_activity.Rmd’

--- re-building ‘DFC_and_HP_and_changing_plots.Rmd’ using rmarkdown
Quitting from lines 20-26 (DFC_and_HP_and_changing_plots.Rmd) 
Error: processing vignette 'DFC_and_HP_and_changing_plots.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘DFC_and_HP_and_changing_plots.Rmd’

--- re-building ‘Loading_and_preprocessing_data_in_DigiRhythm.Rmd’ using rmarkdown
trying URL 'https://raw.githubusercontent.com/nasserdr/digiRhythm_sample_datasets/main/516b_2.csv'
Content type 'text/plain; charset=utf-8' length 2655404 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

--- finished re-building ‘Loading_and_preprocessing_data_in_DigiRhythm.Rmd’

SUMMARY: processing the following files failed:
  ‘Actgram_diurnality_avg_activity.Rmd’
  ‘DFC_and_HP_and_changing_plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘zinbwave’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls not declared from:
  ‘MASS’ ‘Matrix’ ‘NNMF’ ‘RANN’ ‘RSpectra’ ‘c’ ‘coRanking’ ‘ggplot’
  ‘igraph’ ‘loe’ ‘scales’ ‘tidyr’
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
installed size is 58.3Mb
  sub-directories of 1Mb or more:
    libs  57.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
'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.
Package required but not available: ‘supraHex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.8Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  11.6Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rjson’ ‘uuid’
  All declared Imports should be used.
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    data      2.0Mb
    extdata   2.3Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Packages suggested but not available for checking: 'doMPI', 'doRedis'
Package unavailable to check Rd xrefs: ‘doMPI’
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘ggplot2’ ‘lattice’ ‘latticeExtra’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'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:
    libs   7.5Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    tutorials   5.2Mb
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.6Mb
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 288.0Mb
  sub-directories of 1Mb or more:
    libs  287.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    doc    1.7Mb
    libs  25.9Mb
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Codoc mismatches from documentation object 'IQLearnFS_VHet-methods':
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
Package suggested but not available for checking: ‘hdf5r’
Note: found 9 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   8.5Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs       10.6Mb
    shiny_app   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bayestestR’ ‘correlation’ ‘datawizard’ ‘effectsize’ ‘modelbased’
  ‘parameters’ ‘performance’ ‘report’ ‘see’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1409 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’ ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘econet.tex’ using tex
Error: processing vignette 'econet.tex' failed with diagnostics:
Running 'texi2dvi' on 'econet.tex' failed.
LaTeX errors:
! LaTeX Error: File `orcidlink.sty' not found.

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 107.0Mb
  sub-directories of 1Mb or more:
    libs  106.3Mb
GNU make is a SystemRequirements.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112'): paVector ────────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
Note: found 7 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown
Warning: Removed 12 rows containing missing values (geom_point).
Warning: Removed 12 rows containing missing values (geom_label).
! Missing endcsname inserted.
<to be read again> 
                   unhbox 
l.293 \includegraphics{./images/Figure_1.png}

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocStyle’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
installed size is 142.4Mb
  sub-directories of 1Mb or more:
    libs  142.3Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  59.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2jags’
Note: found 50 marked Latin-1 strings
'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:
    libs  14.8Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  19.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Note: found 9451 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘sp’ ‘testthat’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    libs   2.2Mb
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    java   1.3Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mzR’
Namespaces in Imports field not imported from:
  ‘methods’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.7Mb
    libs   2.4Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMMAgeo’ ‘limSolve’ ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘matrixStats’
  All declared Imports should be used.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
'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:
    extdata   4.0Mb
Package suggested but not available for checking: ‘RODBC’
Package unavailable to check Rd xrefs: ‘RODBC’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Note: found 595 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
'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   6.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’ ‘tidyquant’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running ‘testthat.R’ [18s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_helper_blocksize.R:34'): blockSize reports block size in row-col order ──
  Error: [writeRaster] invalid driver
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_helper_blocksize.R:34:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─terra::writeRaster(...) at test_helper_blocksize.R:35:4
   4. └─terra::writeRaster(...)
   5.   └─terra (local) .local(x, filename, ...)
   6.     └─terra:::messages(x, "writeRaster")
   7.       └─terra:::error(f, x@ptr$getError())
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 463 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    exiftool  14.0Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/expss.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
installed size is  8.6Mb
  sub-directories of 1Mb or more:
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    libs   5.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    doc    1.0Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1430 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.9Mb
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
Package suggested but not available for checking: ‘coxKM’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.5Mb
Package suggested but not available for checking: ‘NNLM’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘fst’ ‘kit’ ‘magrittr’ ‘matrixStats’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   6.7Mb
Unexported objects imported by ':::' calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Note: found 75 marked UTF-8 strings
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/fdaPDE.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.2Mb
Note: found 76 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
'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:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 43825 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nflreadr’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 39.5Mb
  sub-directories of 1Mb or more:
    libs  37.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         5.0Mb
    doc       2.2Mb
    extdata   2.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.0Mb
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    lib   10.4Mb
    libs  19.6Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.6Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘evaluate’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 82 marked UTF-8 strings
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 300.6Mb
  sub-directories of 1Mb or more:
    libs  299.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' call not declared from: ‘q’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 55.6Mb
  sub-directories of 1Mb or more:
    libs  54.5Mb
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘minet’
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘Rcpp’ ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rgeos’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.4Mb
    libs   7.5Mb
Namespace in Imports field not imported from: ‘RCSF’
  All declared Imports should be used.
Note: found 31 marked UTF-8 strings
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fable’ ‘fabletools’ ‘feasts’ ‘ggplot2’ ‘lubridate’ ‘tibble’
  ‘tidyr’ ‘tsibble’ ‘tsibbledata’ ‘urca’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
    libs   5.5Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 81.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.5Mb
    libs  73.5Mb
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘foba’
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
Running examples in ‘fsMTS-Ex.R’ failed
The error most likely occurred in:

> ### Name: fsEnsemble
> ### Title: Ensemble feature selection for MTS
> ### Aliases: fsEnsemble
> 
> ### ** Examples
> 
> 
> # Load traffic data
> data(traffic.mini)
> 
> # Scaling is sometimes useful for feature selection
> # Exclude the first column - it contains timestamps
> data <- scale(traffic.mini$data[,-1])
> 
> mIndep<-fsMTS(data, max.lag=3, method="ownlags")
> mCCF<-fsMTS(data, max.lag=3, method="CCF")
> mDistance<-fsMTS(data, max.lag=3, method="distance", shortest = traffic.mini$shortest, step = 5)
> mGLASSO<-fsMTS(data, max.lag=3,method="GLASSO", rho = 0.05)
> mLARS<-fsMTS(data, max.lag=3,method="LARS")
> mRF<-fsMTS(data, max.lag=3,method="RF")
> mMI<-fsMTS(data, max.lag=3,method="MI")
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so':
  dlopen(/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so, 6): Library not loaded: /opt/R/arm64/gfortran/lib/libquadmath.0.dylib
  Referenced from: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so
  Reason: image not found
Calls: fsMTS -> fsMI -> loadNamespace -> library.dynam -> dyn.load
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘simulated.Rmd’ using rmarkdown
Loading required package: sparsevar
Loading required package: fsMTS
Loading required package: plot.matrix
Loading required package: svMisc

Attaching package: 'svMisc'

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

    ?

Loading required package: MTS
Quitting from lines 114-120 (simulated.Rmd) 
Error: processing vignette 'simulated.Rmd' failed with diagnostics:
unable to load shared object '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so':
  dlopen(/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so, 6): Library not loaded: /opt/R/arm64/gfortran/lib/libquadmath.0.dylib
  Referenced from: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so
  Reason: image not found
--- failed re-building ‘simulated.Rmd’

--- re-building ‘traffic.Rmd’ using rmarkdown
Loading required package: fsMTS
Loading required package: plot.matrix
Loading required package: svMisc

Attaching package: 'svMisc'

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

    ?

Loading required package: MTS
Quitting from lines 65-68 (traffic.Rmd) 
Error: processing vignette 'traffic.Rmd' failed with diagnostics:
unable to load shared object '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so':
  dlopen(/Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so, 6): Library not loaded: /opt/R/arm64/gfortran/lib/libquadmath.0.dylib
  Referenced from: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/mpmi/libs/mpmi.so
  Reason: image not found
--- failed re-building ‘traffic.Rmd’

SUMMARY: processing the following files failed:
  ‘simulated.Rmd’ ‘traffic.Rmd’

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘WGCNA’
'LazyData' is specified without a 'data' directory
File ‘fuzzyRankTests/libs/fuzzyRankTests.so’:
  Found non-API calls to R: ‘signrank_free’, ‘wilcox_free’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cBioPortalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   6.4Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Package which this enhances but not available for checking: ‘doMPI’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 48.8Mb
  sub-directories of 1Mb or more:
    doc   44.3Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  11.7Mb
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
GNU make is a SystemRequirements.
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     66.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: ‘gputools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 334.5Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    331.2Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lifecycle’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.4Mb
    libs      1.7Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Packages required but not available: 'muscle', 'trackViewer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrvgo’
Namespace in Imports field not imported from: ‘DOSE’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    doc       1.7Mb
    extdata   1.1Mb
    libs      4.0Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyr’
  All declared Imports should be used.
Note: found 80 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 646 marked UTF-8 strings
Note: found 76726 marked UTF-8 strings
installed size is 121.8Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    libs  120.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   6.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.5Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    R        10.0Mb
    extdata   2.5Mb
    help      2.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 49.9Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Packages required but not available: 'cqn', 'topconfects'

Packages suggested but not available for checking:
  'ChAMP', 'dearseq', 'NOISeq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘GWmodel’ ‘beepr’ ‘cartography’ ‘dplyr’ ‘raster’ ‘readxl’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinyjs’ ‘sp’
  ‘spdep’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘scales’ ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘do’ ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  18.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Packages required but not available: 'memes', 'universalmotif'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggOceanMapsData’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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    doc   1.9Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’
  ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’
  ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’
  ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
Note: found 203 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘refund’ ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.4Mb
Namespaces in Imports field not imported from:
  ‘aTSA’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Note: found 1178 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'rtracklayer', 'GenomicRanges', 'BSgenome',
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 134.0Mb
  sub-directories of 1Mb or more:
    libs  133.3Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.2Mb
  sub-directories of 1Mb or more:
    libs  55.5Mb
GNU make is a SystemRequirements.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘GMMBoost’
  All declared Imports should be used.
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs  52.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
installed size is 69.4Mb
  sub-directories of 1Mb or more:
    libs           64.5Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
Malformed Description field: should contain one or more complete sentences.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.7Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.1Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.6Mb
installed size is 148.7Mb
  sub-directories of 1Mb or more:
    libs  147.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘utils’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.9Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'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 Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hexSticker’
Package suggested but not available for checking: ‘monocle’
Namespace in Imports field not imported from: ‘lfc’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘monocle’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cubature’ ‘magicaxis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘quadmesh’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Note: found 989 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.9Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   3.6Mb
Note: found 116 marked UTF-8 strings
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.7Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 195.6Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    java  192.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs    1.5Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package suggested but not available for checking: ‘Rmpi’
Note: found 8248 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
'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 10.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘questionr’ ‘rprojroot’ ‘tidyverse’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
'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  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Namespaces in Imports field not imported from:
  ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’ ‘healthyR.ts’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Heatplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  18.8Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Package suggested but not available for checking: ‘marray’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat.linnet’
  All declared Imports should be used.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
    libs     11.0Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
':::' call which should be '::': ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs       10.2Mb
Package suggested but not available for checking: ‘INLA’
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  45.7Mb
'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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
installed size is 41.0Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
GNU make is a SystemRequirements.
Note: found 9638 marked UTF-8 strings
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    help   2.3Mb
    libs   2.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 84.7Mb
  sub-directories of 1Mb or more:
    libs  84.2Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘HTSFilter’
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.2Mb
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'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:
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘webshot2’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26215 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   6.7Mb
Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Mmusculus.UCSC.mm10’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
'LazyData' is specified without a 'data' directory
Note: found 329984 marked UTF-8 strings
Package suggested but not available for checking: ‘icd’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 55 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Package suggested but not available for checking: ‘mixAK’
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  35.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Package suggested but not available for checking: ‘ie2miscdata’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   1.2Mb
    libs  15.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         4.4Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     25.0Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs   10.9Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
'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
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Package unavailable to check Rd xrefs: ‘minfi’
'LazyData' is specified without a 'data' directory
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: ‘optimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
BugReports field should be the URL of a single webpage
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘methods’ ‘mlbench’ ‘parallel’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.0Mb
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
Note: found 12106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘testthat’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.1Mb
Note: found 102 marked UTF-8 strings
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
Note: found 12 marked UTF-8 strings
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘Rmpi’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Note: found 1 marked UTF-8 string
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Note: found 7528 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘modules’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  52.6Mb
GNU make is a SystemRequirements.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.1Mb
Note: found 1 marked UTF-8 string
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          19.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.3Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 461377 marked UTF-8 strings
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘knitr’ ‘markdown’
  All declared Imports should be used.
Note: found 85 marked UTF-8 strings
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   7.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    i18n   4.0Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’
  ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.9Mb
Package which this enhances but not available for checking: ‘MRCE’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PSCBS’
Package unavailable to check Rd xrefs: ‘PSCBS’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘boot’ ‘fds’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Note: found 461377 marked UTF-8 strings
Note: found 176 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
Note: found 17 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EBImage’
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    help   2.3Mb
Namespace in Imports field not imported from: ‘keras’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Hs.eg.db’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
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    libs  13.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
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    shiny-landsepi   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    help   1.1Mb
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gof', 'lava.tobit'
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘raster’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘utf8’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RcppProgress’ ‘rgen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Note: found 1096 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Note: found 1 marked UTF-8 string
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  35.9Mb
Note: found 51 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
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    doc   5.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘glue’ ‘stringr’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  11.0Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 94.4Mb
  sub-directories of 1Mb or more:
    libs  93.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  45.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      9.2Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.8Mb
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  45.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 60596 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 435 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Note: found 266 marked UTF-8 strings
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.2Mb
  sub-directories of 1Mb or more:
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    doc        1.6Mb
    libs      22.0Mb
    testdata   1.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.9Mb
  sub-directories of 1Mb or more:
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Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 994 marked Latin-1 strings
Package suggested but not available for checking: ‘RDRToolbox’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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    libs      1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GeneticsPed’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Note: found 55 marked UTF-8 strings
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
'LazyData' is specified without a 'data' directory
installed size is 53.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  50.9Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 2096 marked UTF-8 strings
Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is 72.5Mb
  sub-directories of 1Mb or more:
    libs  72.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Note: found 134 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘maptools’ ‘sp’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.2Mb
installed size is 142.8Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    libs  135.5Mb
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Note: found 41 marked UTF-8 strings
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
    libs   5.8Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17524 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Note: found 55 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Package suggested but not available for checking: ‘showtext’
Note: found 11396 marked UTF-8 strings
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         19.6Mb
installed size is 36.7Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Note: found 29618 marked UTF-8 strings
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   3.1Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 55 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.4Mb
Note: found 996 marked UTF-8 strings
Note: found 13062 marked UTF-8 strings
Note: found 1763 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Note: found 5210 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      12.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
--- re-building ‘an_introduction_to_markovchain_package.Rmd’ using rmarkdown
Package:  markovchain
Version:  0.9.0
Date:     2022-07-01
BugReport: https://github.com/spedygiorgio/markovchain/issues

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

! Emergency stop.
<read *> 

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

--- re-building ‘gsoc_2017_additions.Rmd’ using rmarkdown
Package:  markovchain
Version:  0.9.0
Date:     2022-07-01
BugReport: https://github.com/spedygiorgio/markovchain/issues

--- finished re-building ‘gsoc_2017_additions.Rmd’

--- re-building ‘higher_order_markov_chains.Rmd’ using rmarkdown
Loading required package: markovchain
Package:  markovchain
Version:  0.9.0
Date:     2022-07-01
BugReport: https://github.com/spedygiorgio/markovchain/issues

This function is experimental
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

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

SUMMARY: processing the following files failed:
  ‘an_introduction_to_markovchain_package.Rmd’
  ‘higher_order_markov_chains.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘wiggleplotr’
Package suggested but not available for checking: ‘flashr’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
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Package suggested but not available for checking: ‘gurobi’
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
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installed size is 11.4Mb
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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
installed size is  9.4Mb
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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
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 18 marked UTF-8 strings
Note: found 17 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Note: found 66 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
installed size is 18.6Mb
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Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?

  ‘mcemGLM-vignette.Rnw’... failed to complete the test
installed size is  5.4Mb
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Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 46 marked UTF-8 strings
installed size is  5.6Mb
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installed size is 36.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.4Mb
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installed size is  7.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/mcr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 20.0Mb
  sub-directories of 1Mb or more:
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Note: found 7757 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 123.5Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.2Mb
  sub-directories of 1Mb or more:
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installed size is 103.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 117.0Mb
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GNU make is a SystemRequirements.
Note: found 37 marked UTF-8 strings
Package suggested but not available for checking: ‘genuMet’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package suggested but not available for checking: ‘EBImage’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘hgu133a.db’
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 22.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 84.4Mb
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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Note: found 2 marked UTF-8 strings
installed size is  7.8Mb
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'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
installed size is 26.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
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Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘webshot2’
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is 21.3Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProteoMM’
Package unavailable to check Rd xrefs: ‘DAPAR’
installed size is  7.6Mb
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Note: found 9345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dada2’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
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Namespaces in Imports field not imported from:
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installed size is 20.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
installed size is  5.0Mb
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installed size is  7.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
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Namespace in Imports field not imported from: ‘stats’
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 91.8Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
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Namespace in Imports field not imported from: ‘mcmcr’
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Namespace in Imports field not imported from: ‘grDevices’
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Package suggested but not available for checking: ‘RODBC’
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Package which this enhances but not available for checking: ‘pbdMPI’
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Namespace in Imports field not imported from: ‘rlang’
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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 12.0Mb
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Namespace in Imports field not imported from: ‘RColorBrewer’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘genefilter’
Namespace in Imports field not imported from: ‘reticulate’
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
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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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.2Mb
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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
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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Packages suggested but not available for checking: 'doMPI', 'alstructure'

Package which this enhances but not available for checking: ‘MoBPSmaps’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lazyeval’
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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
Note: found 313 marked UTF-8 strings
Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
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Note: found 18 marked Latin-1 strings
Namespace in Imports field not imported from: ‘parsnip’
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘methods’
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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
installed size is  5.3Mb
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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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.7Mb
Note: found 16 marked UTF-8 strings
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RODBC’
Package unavailable to check Rd xrefs: ‘RODBC’
'LazyData' is specified without a 'data' directory
Note: found 13 marked UTF-8 strings
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs     3.2Mb
    raster   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.2Mb
Note: found 3 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   2.0Mb
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is 93.4Mb
  sub-directories of 1Mb or more:
    libs  93.1Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.5Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   4.5Mb
    libs   3.7Mb
installed size is 57.4Mb
  sub-directories of 1Mb or more:
    libs  56.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  21.0Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtools’ ‘patchwork’ ‘plyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shape’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plsgenomics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘stats’ ‘tidyverse’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
installed size is 106.9Mb
  sub-directories of 1Mb or more:
    libs  106.7Mb
installed size is 129.6Mb
  sub-directories of 1Mb or more:
    doc     4.0Mb
    libs  124.2Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘fields’ ‘optmatch’ ‘rcbalance’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ComplexHeatmap’
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
Note: found 50 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Note: found 63 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Malformed Description field: should contain one or more complete sentences.
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    28.6Mb
    models   1.1Mb
Note: found 47936 marked UTF-8 strings
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘webshot2’
Package suggested but not available for checking: ‘gurobi’
Note: found 5 marked Latin-1 strings
  Note: found 7187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Note: found 140 marked UTF-8 strings
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  19.0Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fastshp’
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.2Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.2Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 194.9Mb
  sub-directories of 1Mb or more:
    libs  194.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Note: found 4894 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              7.1Mb
    classic-bugs   1.5Mb
    include        5.7Mb
    libs          18.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘nlraa’
  All declared Imports should be used.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Package suggested but not available for checking: ‘doMPI’
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'treeio', 'ggtree'
Package unavailable to check Rd xrefs: ‘treeio’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘argparse’ ‘tidyverse’ ‘vcfR’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    libs  16.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
Namespaces in Imports field not imported from:
  ‘rnaturalearthdata’ ‘spocc’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1242 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.1Mb
    libs   3.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Note: found 4 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Package suggested but not available for checking: ‘morse’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.5Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.7Mb
Note: found 32 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/OpenCL.Rcheck/00install.out’ for details.
Note: found 4 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.6Mb
GNU make is a SystemRequirements.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs   11.7Mb
    share  10.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 2524 marked UTF-8 strings
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 210.7Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    libs    199.6Mb
    models    4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Package suggested but not available for checking: ‘openNLPmodels.en’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Note: found 167 marked UTF-8 strings
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   1.3Mb
    libs      5.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.7Mb
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     35.7Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘hrbrthemes’ ‘magrittr’ ‘orthopolynom’ ‘plotly’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.7Mb
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 36 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   5.8Mb
Note: found 263 marked UTF-8 strings
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘jsonlite’
  All declared Imports should be used.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘optparse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scde’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 314 marked UTF-8 strings
Packages which this enhances but not available for checking:
  'CorShrink', 'edgeR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dbplyr’ ‘downloadthis’ ‘ggExtra’ ‘htmlwidgets’ ‘methods’
  ‘rmarkdown’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
Package required but not available: ‘heatmapFlex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.7Mb
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘pathfindR’
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘gplots’ ‘grid’ ‘jetset’ ‘magic’
  ‘msgps’ ‘splines’ ‘stats4’ ‘survival’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   3.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   3.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/pbdMPI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

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

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:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      3.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 153.4Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  149.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘safe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Note: found 11 marked UTF-8 strings
Package suggested but not available for checking: ‘PythonInR’
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs    7.5Mb
    share  12.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ncvreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
'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:
    doc    4.0Mb
    libs  14.0Mb
Note: found 13918 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
installed size is 133.8Mb
  sub-directories of 1Mb or more:
    libs  132.9Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘ptmixed’
Error(s) in re-building vignettes:
  ...
--- re-building ‘pencal-vignette.Rmd’ using rmarkdown
Quitting from lines 158-167 (pencal-vignette.Rmd) 
Error: processing vignette 'pencal-vignette.Rmd' failed with diagnostics:
there is no package called 'ptmixed'
--- failed re-building ‘pencal-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pencal-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   7.7Mb
Namespace in Imports field not imported from: ‘fixest’
  All declared Imports should be used.
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    libs  54.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Note: possible error in 'simplify2array(msg, except = 0L)': unused argument (except = 0) 
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/personalized.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
xgb_cv_personalized: possible error in simplify2array(msg, except =
  0L): unused argument (except = 0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘shinyWidgets’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.1Mb
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.3Mb
Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘cowplot’ ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   2.5Mb
Package suggested but not available for checking: ‘INLA’
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
at_trans : <anonymous>: no visible global function definition for
  ‘viewportTransform’
at_trans : <anonymous>: no visible global function definition for
  ‘groupShear’
at_trans : <anonymous>: no visible global function definition for
  ‘groupFlip’
grobCoords.pp_grobCoords: no visible global function definition for
  ‘emptyGrobCoords’
grobCoords.pp_ps_transformation: no visible global function definition
  for ‘emptyGrobCoords’
makeContent.pp_transformation: no visible global function definition
  for ‘defineGrob’
makeContent.pp_transformation: no visible global function definition
  for ‘useGrob’
transformationGrob: no visible binding for global variable
  ‘viewportTransform’
xylists_to_grobcoords: no visible global function definition for
  ‘emptyGrobCoords’
xylists_to_grobcoords: no visible global function definition for
  ‘gridCoords’
xylists_to_grobcoords : <anonymous>: no visible global function
  definition for ‘gridCoords’
xylists_to_grobcoords: no visible global function definition for
  ‘gridGrobCoords’
Undefined global functions or variables:
  defineGrob emptyGrobCoords gridCoords gridGrobCoords groupFlip
  groupShear useGrob viewportTransform
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2048 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   3.4Mb
    doc   1.2Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pki-x509.c:486:2: warning: 'CC_MD5' is deprecated: first deprecated in macOS 10.15 - This function is cryptographically broken and should not be used in security contexts. Clients should migrate to SHA256 (or stronger). [-Wdeprecated-declarations]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/PKI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘BH’
  All declared Imports should be used.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'monocle3', 'ProjecTILs', 'SeuratWrappers', 'slingshot'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    htmlwidgets   3.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
Note: found 7256 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Note: found 52 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.8Mb
installed size is 56.9Mb
  sub-directories of 1Mb or more:
    libs  56.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘polyRAD’
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R      7.1Mb
    data   4.7Mb
Package unavailable to check Rd xrefs: ‘polyRAD’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      3.6Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
'LazyData' is specified without a 'data' directory
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Package suggested but not available for checking: ‘WhopGenome’
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘psych’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘areal’ ‘microbenchmark’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROI.plugin.symphony’
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.4Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages unavailable to check Rd xrefs: ‘R2jags’, ‘rjags’, ‘jagsUI’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   8.9Mb
Namespace in Imports field not imported from: ‘here’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.4Mb
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 71 marked UTF-8 strings
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
Note: found 42966 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinyApp   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 93457 marked UTF-8 strings
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 165 marked UTF-8 strings
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   6.2Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    4.6Mb
    libs  13.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rio’ ‘shiny’ ‘shinyjs’ ‘utils’ ‘webp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EBImage’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      3.0Mb
'LazyData' is specified without a 'data' directory
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    libs  69.2Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RODBC’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 99.3Mb
  sub-directories of 1Mb or more:
    libs  99.0Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'ALDEx2', 'SDMTools'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Packages suggested but not available for checking:
  'GOSemSim', 'org.Hs.eg.db'
Package suggested but not available for checking: ‘proDA’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘LambertW’ ‘gtools’ ‘mstate’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.4Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘miceadds’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Note: found 26 marked Latin-1 strings
Package required and available but unsuitable version: ‘grDevices’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Note: found 140 marked UTF-8 strings
installed size is 58.9Mb
  sub-directories of 1Mb or more:
    libs  58.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘tweeDEseq’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    doc        4.0Mb
    examples   2.5Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘sjPlot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  56.6Mb
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘PUPAIM-Ex.R’ failed
The error most likely occurred in:

> ### Name: SSLangmuir1analysis
> ### Title: Langmuir Isotherm Nonlinear Analysis via selfStart and Langmuir
> ###   First Linear Model
> ### Aliases: SSLangmuir1analysis
> 
> ### ** Examples
> 
> Ce <- c(0.01353, 0.04648, 0.13239, 0.27714, 0.41600, 0.63607, 0.80435, 1.10327, 1.58223)
> Qe <- c(0.03409, 0.06025, 0.10622, 0.12842, 0.15299, 0.15379, 0.15735, 0.15735, 0.16607)
> SSLangmuir1analysis(Ce,Qe)
Error in (attr(object, "initial"))(mCall = mCall, data = data, LHS = LHS,  : 
  unused arguments (control = list(50, 1e-05, 0.0009765625, FALSE, FALSE, 0, FALSE), trace = FALSE)
Calls: SSLangmuir1analysis
Execution halted
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘lazyeval’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    libs         2.8Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
installed size is 85.5Mb
  sub-directories of 1Mb or more:
    libs  84.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘readxl’ ‘reshape2’ ‘sjmisc’ ‘stringr’ ‘xlsx’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘purrr’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
'LazyData' is specified without a 'data' directory
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     40.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Note: found 4 marked UTF-8 strings
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.6Mb
Note: found 35707 marked UTF-8 strings
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 8504 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘psych’ ‘psychTools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
'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’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc           5.2Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Package suggested but not available for checking: ‘slingshot’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
    libs   1.3Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcompadre’
  All declared Imports should be used.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Warning: Removed 39 row(s) containing missing values (geom_path).
Quitting from lines 425-461 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
'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
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets       10.0Mb
    super-tiny-icons   1.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   4.1Mb
Note: found 7734 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 86.8Mb
  sub-directories of 1Mb or more:
    libs  86.0Mb
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: 'cairoDevice', 'RGtk2'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  11.3Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   4.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
Note: found 8 marked UTF-8 strings
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  37.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 65.1Mb
  sub-directories of 1Mb or more:
    libs  64.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rblpapi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 40.6Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26334 marked UTF-8 strings
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 92.4Mb
  sub-directories of 1Mb or more:
    libs  91.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘rlemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    cont  24.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ROpenOffice', 'RODBC'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.2Mb
    po    2.4Mb
Note: found 345 marked UTF-8 strings
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rcplex.Rcheck/00install.out’ for details.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    include  46.3Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RcppClassic.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      3.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.9Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    include        1.5Mb
    jsonexamples   3.8Mb
    libs          11.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   1.0Mb
    libs      3.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rcrypt.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DeclareDesign’ ‘fabricatr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GOSemSim', 'org.Hs.eg.db'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
Note: found 1036 marked UTF-8 strings
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  15.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      5.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Packages suggested but not available for checking: 'interval', 'Icens'
Package unavailable to check Rd xrefs: ‘interval’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6034 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     19.5Mb
    models    1.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Package suggested but not available for checking: ‘ccdata’
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
Note: found 514 marked UTF-8 strings
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is 51.5Mb
  sub-directories of 1Mb or more:
    libs  50.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 291.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    libs      283.4Mb
    pictures    1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      2.1Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc     1.1Mb
    fonts   1.5Mb
    libs   19.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'showtext', 'sysfonts'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1473 marked UTF-8 strings
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

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

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  18.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RInside.Rcheck/00install.out’ for details.
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_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 104.1Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
    libs     98.5Mb
'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:
    libs  13.5Mb
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  23.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   9.6Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs     17.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.3Mb
'LazyData' is specified without a 'data' directory
installed size is 55.0Mb
  sub-directories of 1Mb or more:
    libs  54.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'GenomicRanges', 'org.Hs.eg.db', 'reactome.db', 'fgsea'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Note: found 31 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RMark.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 134.2Mb
  sub-directories of 1Mb or more:
    libs  133.8Mb
GNU make is a SystemRequirements.
installed size is 91.9Mb
  sub-directories of 1Mb or more:
    libs  91.1Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RmecabKo.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   7.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs       1.4Mb
    minizinc   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
'LazyData' is specified without a 'data' directory
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
GNU make is a SystemRequirements.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘recount3’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    2.2Mb
Missing or unexported object: 'SummarizedExperiment::colnames'
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Note: found 7 marked Latin-1 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘pbdMPI’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Package unavailable to check Rd xrefs: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 113.9Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     111.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  17.7Mb
Note: found 1 marked UTF-8 string
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘bridgesampling’ ‘extraDistr’ ‘psych’ ‘runjags’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘bridgesampling’ ‘runjags’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’ ‘utils’
  All declared Imports should be used.
installed size is 68.0Mb
  sub-directories of 1Mb or more:
    libs  67.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘methods’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 6 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs             31.8Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
'LazyData' is specified without a 'data' directory
sh: cmake: command not found
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    libs  53.7Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rrdrand.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
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    dependencies  20.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  28.0Mb
Note: found 467 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.2Mb
    help   1.4Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
'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:
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
installed size is 187.4Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.8Mb
    libs  179.9Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
GNU make is a SystemRequirements.
installed size is 267.0Mb
  sub-directories of 1Mb or more:
    lib    26.5Mb
    libs  237.6Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Note: found 117 marked UTF-8 strings
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Namespaces in Imports field not imported from:
  ‘bitops’ ‘httpuv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is 108.4Mb
  sub-directories of 1Mb or more:
    libs  108.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmarkdown   6.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs       2.4Mb
    projects   2.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Note: found 9 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data      4.1Mb
    extdata   1.4Mb
    libs      4.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'showtext', 'sysfonts'
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘plyr’ ‘terra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
installed size is 58.2Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘lubridate’ ‘rstantools’
  All declared Imports should be used.
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   8.1Mb
'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   4.7Mb
'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   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.8Mb
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘rWikiPathways’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     57.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/RVowpalWabbit.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Note: found 2016 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs    9.9Mb
    yacas   1.3Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs   10.9Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 37 marked Latin-1 strings
  Note: found 172 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 63 marked Latin-1 strings
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Note: found 120 marked UTF-8 strings
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  12.3Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
'LazyData' is specified without a 'data' directory
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  42.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.4Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'org.Sc.sgd.db'
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.4Mb
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.3Mb
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'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
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Found the following executable file:
  inst/extdata/Azores.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pcalg’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘cowplot’ ‘easypackages’ ‘plyr’ ‘readr’ ‘stringr’
  ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocSingular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Nebulosa', 'infercnv'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘oligoClasses’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘Matrix’ ‘SingleCellExperiment’ ‘SummarizedExperiment’
  ‘ggsci’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.0Mb
Note: found 3 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  15.2Mb
GNU make is a SystemRequirements.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rsbml’
Packages required but not available: 'ArrayExpress', 'tximport'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixOmics’
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   2.6Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs    24.1Mb
    models   1.6Mb
Note: found 836 marked UTF-8 strings
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.3Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.3Mb
Note: found 3128 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Packages suggested but not available for checking:
  'GenomicAlignments', 'GenomicRanges', 'muscle', 'Rsamtools'
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.3Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘monocle’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespace in Imports field not imported from: ‘geometries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 301.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    libs    295.3Mb
    sqlite    1.5Mb
Package which this enhances but not available for checking: ‘polynom’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.9Mb
Found the following executable files:
  inst/extdata/existing.dbf
  inst/extdata/existingna.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘huge’
  All declared Imports should be used.
Package suggested but not available for checking: ‘hydromad’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    www   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 2397 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package suggested but not available for checking: ‘copynumber’
Package required and available but unsuitable version: ‘GenomeInfoDb’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
GNU make is a SystemRequirements.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  11.7Mb
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Package suggested but not available for checking: ‘clipper’
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  21.4Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'SummarizedExperiment', 'SingleCellExperiment'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   7.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following executable file:
  inst/extdata/shapefiles/df_bsb/df_bsb.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.0Mb
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

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

Probably some imports need to be declared in the NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘CompQuadForm’ ‘boot’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.1Mb
GNU make is a SystemRequirements.
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 1122 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.4Mb
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
Packages suggested but not available for checking:
  'SNPlocs.Hsapiens.dbSNP144.GRCh38', 'MafDb.1Kgenomes.phase3.GRCh38'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      3.3Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘itertools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘devtools’ ‘stats’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.1Mb
    libs  10.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘sos.Rnw’ using Sweave
Loading required package: brew

Attaching package: 'sos'

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

    ?
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Package suggested but not available for checking: ‘DropletUtils’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  13.5Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.1Mb
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  36.9Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    java   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘spatstat.core’ ‘spatstat.linnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is 54.6Mb
  sub-directories of 1Mb or more:
    libs  53.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.5Mb
Note: found 283 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘pheatmap’ ‘stats’ ‘viridis’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.8Mb
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Package unavailable to check Rd xrefs: ‘spatstat.model’
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   1.9Mb
Packages unavailable to check Rd xrefs: ‘spatstat.model’, ‘spatstat.explore’
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'spatstat.explore', 'spatstat.model'
Packages unavailable to check Rd xrefs: ‘spatstat.model’, ‘spatstat.explore’
Package suggested but not available for checking: ‘spatstat.model’
Package unavailable to check Rd xrefs: ‘spatstat.model’
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
Note: found 56 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
Note: found 34 marked UTF-8 strings
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
    etc   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Found the following executable files:
  inst/extdata/SouthernBuh-habitats_shapefile.dbf
  inst/extdata/test_shapefile.dbf
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘spFSR-Ex.R’ failed
The error most likely occurred in:

> ### Name: spFeatureSelection
> ### Title: SPSA-FSR for Feature Selection and Ranking
> ### Aliases: spFeatureSelection
> 
> ### ** Examples
> 
> 
> library(mlr3)          # load the mlr3 package
> library(mlr3learners) # load the mlr3learners package
> 
> task    <- tsk('iris') # define task
> wrapper <- lrn('classif.rpart')                # define wrapper
> measure <- msr('classif.acc')
> 
> # run spsa
> spsaMod <- spFeatureSelection( task = task,
+                                wrapper = wrapper,
+                                scoring = measure,
+                                num.features.selected = 3,
+                                n.jobs = 1,
+                                iters.max = 2,
+                                num.grad.avg = 1)
Error in .mapply(.f, .dots, .args) : 
  zero-length inputs cannot be mixed with those of non-zero length
Calls: spFeatureSelection ... .__Task__add_strata -> pmap_dtc -> mapply_list -> .mapply
Execution halted
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Note: found 189 marked UTF-8 strings
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘psy’ ‘ranger’
  All declared Imports should be used.
Package suggested but not available for checking: ‘antaresViz’
Package unavailable to check Rd xrefs: ‘antaresViz’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs     12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7587 marked UTF-8 strings
Namespace in Imports field not imported from: ‘batchtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggridges’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘rgeoda’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is 59.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  57.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’ ‘spatstat.linnet’ ‘spatstat.sparse’
  ‘spatstat.utils’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs  10.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.4Mb
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   1.0Mb
    libs  26.1Mb
'LazyData' is specified without a 'data' directory
installed size is 97.9Mb
  sub-directories of 1Mb or more:
    libs  97.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Note: found 40748 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 302-324 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
duplicated values in No.pas
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs  53.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       2.0Mb
installed size is 85.8Mb
  sub-directories of 1Mb or more:
    libs  85.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyselect’
  All declared Imports should be used.
Package suggested but not available for checking: ‘starsdata’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   1.7Mb
    nc    1.7Mb
Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> ### Name: st_warp
> ### Title: Warp (resample) grids in stars objects to a new grid, possibly
> ###   in an new coordinate reference system
> ### Aliases: st_warp
> 
> ### ** Examples
> 
> geomatrix = system.file("tif/geomatrix.tif", package = "stars")
> (x = read_stars(geomatrix))
stars object with 2 dimensions and 1 attribute
attribute(s):
               Min. 1st Qu. Median    Mean 3rd Qu. Max.
geomatrix.tif    74     107    123 126.765     132  255
dimension(s):
  from to  offset delta                refsys point values x/y
x    1 20 1841002   1.5 WGS 84 / UTM zone 11N  TRUE   NULL [x]
y    1 20 1144003  -1.5 WGS 84 / UTM zone 11N  TRUE   NULL [y]
sheared raster with parameters: -5 -5 
> new_crs = st_crs(4326)
> y = st_warp(x, crs = new_crs)
> plot(st_transform(st_as_sfc(st_bbox(x)), new_crs), col = NA, border = 'red')
> plot(st_as_sfc(y, as_points=FALSE), col = NA, border = 'green', axes = TRUE, add = TRUE)
> image(y, add = TRUE, nbreaks = 6)
> plot(st_as_sfc(y, as_points=TRUE), pch=3, cex=.5, col = 'blue', add = TRUE)
> plot(st_transform(st_as_sfc(x, as_points=FALSE), new_crs), add = TRUE)
> # warp 0-360 raster to -180-180 raster:
> r = read_stars(system.file("nc/reduced.nc", package = "stars"))
trying to read file: /Volumes/Builds/packages/big-sur-arm64/results/4.1/stars.Rcheck/stars/nc/reduced.nc
Error in CPL_read_gdal(as.character(x), as.character(options), as.character(driver),  : 
  file not found
Calls: read_stars ... is_big -> read_stars -> <Anonymous> -> CPL_read_gdal
Execution halted
Running ‘aggregate.R’ [1s/2s]
  Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4
< Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 8.2.1; sf_use_s2() is TRUE
---
> Linking to GEOS 3.10.2, GDAL 3.4.3, PROJ 8.2.0; sf_use_s2() is TRUE
  Running ‘align.R’ [1s/1s]
  Comparing ‘align.Rout’ to ‘align.Rout.save’ ... OK
  Running ‘area.R’ [1s/1s]
  Comparing ‘area.Rout’ to ‘area.Rout.save’ ... OK
  Running ‘crop.R’ [2s/2s]
  Comparing ‘crop.Rout’ to ‘crop.Rout.save’ ... OK
  Running ‘curvilinear.R’ [1s/1s]
  Comparing ‘curvilinear.Rout’ to ‘curvilinear.Rout.save’ ... OK
  Running ‘datasets.R’ [1s/1s]
  Comparing ‘datasets.Rout’ to ‘datasets.Rout.save’ ... OK
  Running ‘dimensions.R’ [1s/1s]
Running the tests in ‘tests/dimensions.R’ failed.
Complete output:
  > # https://github.com/r-spatial/stars/issues/295
  > suppressPackageStartupMessages(library(stars))
  > raw <- read_stars(system.file("nc/bcsd_obs_1999.nc", package = "stars"))
  trying to read file: /Volumes/Builds/packages/big-sur-arm64/results/4.1/stars.Rcheck/stars/nc/bcsd_obs_1999.nc
  Error in CPL_read_gdal(as.character(x), as.character(options), as.character(driver),  : 
    file not found
  Calls: read_stars ... is_big -> read_stars -> <Anonymous> -> CPL_read_gdal
  Execution halted
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 18 marked UTF-8 strings
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.4Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.2Mb
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Note: found 52 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Package required but not available: ‘pvca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
Missing link or links in documentation object 'print.std_selected.Rd':
  ‘print.lm’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Data codoc mismatches from documentation object 'SLCS':
Variables in data frame 'SLCS'
  Code: SLCS_1 SLCS_10 SLCS_11 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
  Docs: SLCS_11 SLCS_1 SLCS_10 SLCS_12 SLCS_13 SLCS_14 SLCS_15 SLCS_16
        SLCS_2 SLCS_3 SLCS_4 SLCS_5 SLCS_6 SLCS_7 SLCS_8 SLCS_9 age sex
        user_id
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.8Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   8.0Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘Rsymphony’
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   9.9Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Note: found 83 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc  12.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mixtools’ ‘parallel’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocParallel’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    2.3Mb
    libs   1.6Mb
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Package suggested but not available for checking: ‘INLA’
installed size is 151.6Mb
  sub-directories of 1Mb or more:
    libs  150.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggtree’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.1Mb
    doc    3.4Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Note: found 25 marked UTF-8 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Package unavailable to check Rd xrefs: ‘survJamda’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   8.6Mb
DNF: multiple local function definitions for ‘mu_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘mu_y’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_x’ with different
  formal arguments
DNF: multiple local function definitions for ‘sigma_y’ with different
  formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_x’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘mu_y’ with
  different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_x’
  with different formal arguments
DNFOptim : MLE_f: multiple local function definitions for ‘sigma_y’
  with different formal arguments
modelSim: multiple local function definitions for ‘mu_x’ with different
  formal arguments
modelSim: multiple local function definitions for ‘mu_y’ with different
  formal arguments
modelSim: multiple local function definitions for ‘sigma_x’ with
  different formal arguments
modelSim: multiple local function definitions for ‘sigma_y’ with
  different formal arguments
'LazyData' is specified without a 'data' directory
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘swephRdata’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is 50.3Mb
  sub-directories of 1Mb or more:
    libs  49.4Mb
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘udunits2’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    fonts   1.7Mb
    libs   15.5Mb
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 81 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked Latin-1 strings
  Note: found 1270 marked UTF-8 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 137 marked UTF-8 strings
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dearseq’
Package unavailable to check Rd xrefs: ‘dearseq’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  35.7Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    apps   2.3Mb
    libs  10.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  18.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       3.7Mb
    libs      2.4Mb
    telemac   1.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is 345.4Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs  342.2Mb
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.6Mb
    tessdata  22.2Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.0Mb
    libs   4.2Mb
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Note: found 3 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.8Mb
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sysfonts', 'showtext'
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    data   3.1Mb
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           1.6Mb
    htmlwidgets   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  56.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’ ‘tidybins’ ‘validata’
  All declared Imports should be used.
Note: found 4546 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  60.3Mb
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   4.4Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs    12.0Mb
    tiledb  20.6Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2750 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  44.7Mb
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.4Mb
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    examples  12.0Mb
    include    3.5Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘torch’
  All declared Imports should be used.
installed size is 199.9Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       1.6Mb
    include    1.5Mb
    libs     190.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

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

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

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

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

Attaching package: 'fda'

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

    matplot

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

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
  Note: found 701 marked UTF-8 strings
Package suggested but not available for checking: ‘taxidata’
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
'LazyData' is specified without a 'data' directory
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  49.1Mb
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    libs   2.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    libs       1.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.3Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 139.4Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    libs  134.5Mb
'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
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ez’ ‘forcats’ ‘ggplot2’
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
installed size is 95.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  92.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       21.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   4.3Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
'LazyData' is specified without a 'data' directory
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls not declared from:
  ‘unitizerdummypkg1’ ‘unitizerdummypkg2’
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 47.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  43.5Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lavaan’ ‘lifecycle’ ‘patchwork’ ‘ragg’ ‘scales’ ‘simstandard’
  All declared Imports should be used.
Note: found 7872 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USAboundariesData’
Package suggested but not available for checking: ‘USA.state.boundaries.data’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   6.6Mb
Note: found 1 marked UTF-8 string
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 33 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  23.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking:
  'vaersNDvax', 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 128 marked UTF-8 strings
Note: found 49 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    help   3.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  53.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.0Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘colorspace’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  60.6Mb
Note: found 4954 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 85.8Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘ecospat’ ‘jsonlite’
  ‘leaflet.extras’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’ ‘sp’
  ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.3Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1668 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3984 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 6738 marked UTF-8 strings
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocParallel’
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.4Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘vdiffr’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   7.9Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    bin   4.2Mb
    lib   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  43.6Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    java  27.2Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
installed size is 50.9Mb
  sub-directories of 1Mb or more:
    libs  50.6Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 48.8Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘XML’ ‘atom4R’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Package suggested but not available for checking: ‘SDMTools’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 87.4Mb
  sub-directories of 1Mb or more:
    libs  86.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Note: found 596 marked UTF-8 strings
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘patchwork’
  All declared Imports should be used.
Package required but not available: ‘BSgenome.Mmusculus.UCSC.mm10’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       3.0Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Package suggested but not available for checking: ‘HiTC’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `SimGR(PrepGR = PrepTotNA, Param = c(270.426, 0.984, 108.853, 
      2.149), EffCrit = "KGE2", WupPer = c("1994-01-01", "1994-12-31"), 
      SimPer = c("1995-01-01", "1998-12-31"))`: Non convenient date for the warm-up period "WupPer"
  Backtrace:
      ▆
   1. ├─testthat::expect_warning(...) at test-SimGR.R:28:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─airGRteaching::SimGR(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
'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
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 231 marked UTF-8 strings
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    test_v8    2.0Mb
    testdata   2.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 87.9Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs  82.5Mb
Note: found 1409 marked UTF-8 strings
Package which this enhances but not available for checking: ‘ARTP’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 899 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘autocart-intro.Rmd’ using rmarkdown
Loading required package: fields
Loading required package: spam
Spam version 2.8-0 (2022-01-05) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite

Try help(fields) to get started.
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘AzureKeyVault’
Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘baffle.Rmd’ using rmarkdown
Quitting from lines 88-95 (baffle.Rmd) 
Error: processing vignette 'baffle.Rmd' failed with diagnostics:
unused arguments (title.font = 2, title.cex = 1.5)
--- failed re-building ‘baffle.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 74.6Mb
  sub-directories of 1Mb or more:
    libs  72.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is 67.6Mb
  sub-directories of 1Mb or more:
    libs  66.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/bapred.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.4Mb
Package required and available but unsuitable version: ‘warbleR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.3Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dbplyr’ ‘dotenv’ ‘googleAuthR’ ‘writexl’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GO.db', 'org.Hs.eg.db', 'reactome.db'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
installed size is 61.8Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 42.8Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 83.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  82.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.2Mb
installed size is 69.4Mb
  sub-directories of 1Mb or more:
    libs  68.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 83.6Mb
  sub-directories of 1Mb or more:
    libs  82.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
GNU make is a SystemRequirements.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  14.4Mb
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  19.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Namespace in Imports field not imported from: ‘RcppNumerical’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  15.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.5Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
GNU make is a SystemRequirements.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘rgl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BRugs’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 79.0Mb
  sub-directories of 1Mb or more:
    libs  77.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  43.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  56.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Note: found 10089 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    help   1.1Mb
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   6.2Mb
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 146.6Mb
  sub-directories of 1Mb or more:
    include  146.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.3Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Note: found 940 marked Latin-1 strings
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Checking should be performed on sources prepared by ‘R CMD build’.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespace in Imports field not imported from: ‘runonce’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.9Mb
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help   1.5Mb
    libs   4.7Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  18.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is 75.3Mb
  sub-directories of 1Mb or more:
    libs  74.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘desc’ ‘lme4’ ‘mitml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      2.8Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Note: found 46 marked UTF-8 strings
Package suggested but not available for checking: ‘rpanel’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Package suggested but not available for checking: ‘IHW’
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    libs  38.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘digest’ ‘ergm’ ‘foreign’ ‘gWidgets2’ ‘gWidgets2tcltk’ ‘haven’
  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    libs  71.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.8Mb
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   7.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'::' or ':::' import not declared from: ‘StochBlockTest’
'library' or 'require' call not declared from: ‘StochBlockTest’
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
installed size is 123.0Mb
  sub-directories of 1Mb or more:
    libs  122.2Mb
GNU make is a SystemRequirements.
installed size is 78.3Mb
  sub-directories of 1Mb or more:
    libs  77.7Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  44.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 76.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  69.3Mb
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Package suggested but not available for checking: ‘sangerseqR’
installed size is 375.3Mb
  sub-directories of 1Mb or more:
    include    8.8Mb
    lib      366.1Mb
GNU make is a SystemRequirements.
installed size is 78.3Mb
  sub-directories of 1Mb or more:
    libs  77.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is 80.6Mb
  sub-directories of 1Mb or more:
    libs  80.4Mb
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Note: found 2487 marked UTF-8 strings
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.9Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: ‘glmmADMB’
Found the following significant warnings:
  Warning: multiple methods tables found for ‘export’
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/Brundle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    help   1.3Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    fonts   3.1Mb
    lib     4.9Mb
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs  27.6Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 95.9Mb
  sub-directories of 1Mb or more:
    libs  95.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 49.6Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qgraph’ ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is 61.9Mb
  sub-directories of 1Mb or more:
    libs  61.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Note: found 287 marked UTF-8 strings
Note: found 512 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Note: found 1 marked UTF-8 string
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘reshape2’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  27.3Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.4Mb
'LazyData' is specified without a 'data' directory
installed size is 132.5Mb
  sub-directories of 1Mb or more:
    libs  132.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    duckdb   3.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
Namespace in Imports field not imported from: ‘urltools’
  All declared Imports should be used.
Note: found 907 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.4Mb
    libs   9.9Mb
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GLAD’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘CGNM-vignette.Rmd’ using rmarkdown
Quitting from lines 36-57 (CGNM-vignette.Rmd) 
Error: processing vignette 'CGNM-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'RxODE':
 .onLoad failed in loadNamespace() for 'RxODE', details:
  call: NULL
  error: RxODE compiled with PreciseSums '0.4' but PreciseSums '0.5' is loaded
Recompile RxODE with the this version of PreciseSums
--- failed re-building ‘CGNM-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘CGNM-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GenomicInteractions', 'countreg'
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Package required but not available: ‘TxDb.Mmusculus.UCSC.mm10.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28982 marked UTF-8 strings
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_clipp.Rmd’ using rmarkdown
Error: processing vignette 'using_clipp.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘using_clipp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘methods’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'GO.db', 'moe430a.db'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 4622 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Note: found 19 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 30244 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘formatR’ ‘jsonlite’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/cold.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘CAM’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.9Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
installed size is 58.4Mb
  sub-directories of 1Mb or more:
    libs  57.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs          2.8Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.4Mb
Note: found 139613 marked UTF-8 strings
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
Note: found 1934235 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Note: found 2385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Note: found 20 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.3Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked UTF-8 strings
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer2’
Namespaces in Imports field not imported from:
  ‘DT’ ‘gbm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package required but not available: ‘EnsDb.Hsapiens.v79’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 500 marked UTF-8 strings
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Note: found 282 marked UTF-8 strings
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Note: found 3031 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 1350 marked UTF-8 strings
installed size is 138.1Mb
  sub-directories of 1Mb or more:
    R       1.2Mb
    data    1.6Mb
    libs  134.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    demos         4.3Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘fs’ ‘googleCloudStorageR’
  All declared Imports should be used.
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    deps  10.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.9Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 8 marked Latin-1 strings
installed size is 58.8Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
Package suggested but not available for checking: ‘msa’
Note: found 2596 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54315 marked UTF-8 strings
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.7Mb
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘bslib’ ‘knitr’ ‘matrixStats’ ‘rmarkdown’ ‘shinythemes’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.4Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘plyr’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  56.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 8014 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls not declared from:
  ‘MASS’ ‘Matrix’ ‘NNMF’ ‘RANN’ ‘RSpectra’ ‘c’ ‘coRanking’ ‘ggplot’
  ‘igraph’ ‘loe’ ‘scales’ ‘tidyr’
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  56.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:158'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 31 - 28 == 3
  ── Failure ('test-realized_duration.R:161'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 31 - 28 == 3
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package suggested but not available for checking: ‘BOLTSSIRR’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.2Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  11.6Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rjson’ ‘uuid’
  All declared Imports should be used.
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Packages suggested but not available for checking: 'doMPI', 'doRedis'
Package unavailable to check Rd xrefs: ‘doMPI’
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘ggplot2’ ‘lattice’ ‘latticeExtra’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Running ‘simpleTests.R’ [0s/0s]
  Running ‘skeleton_git2r.R’ [3s/3s]
Running the tests in ‘tests/skeleton_git2r.R’ failed.
Last 13 lines of output:
  * saving partial Rd database
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘foo_1.0.tar.gz’
  
  dratting
  Added and committed foo_1.0.tar.gz plus PACKAGES files. Still need to push.
  
  Error in testRepoActions(repodir) : 
    Wrong package files found after pruning for version = NA
  Calls: runTest -> testRepoActions
  In addition: Warning message:
  In (function (dir = ".", fields = NULL, type = c("source", "mac.binary",  :
    PACKAGES files do not include MD5 sums in the win.binary case, so strict checking is impossible. Calling down to write_PACKAGES directly.
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    tutorials   5.2Mb
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   8.1Mb
'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:
    appinformation   4.1Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.6Mb
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.0Mb
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 261.9Mb
  sub-directories of 1Mb or more:
    libs  261.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  24.1Mb
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   3.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Codoc mismatches from documentation object 'IQLearnFS_VHet-methods':
\S4method{qqplot}{IQLearnFS_VHet}
  Code: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ...)
  Docs: function(x, y, plot.it = TRUE, xlab = deparse1(substitute(x)),
                 ylab = deparse1(substitute(y)), ..., conf.level =
                 NULL, conf.args = list(exact = NULL, simulate.p.value
                 = FALSE, B = 2000, col = NA, border = NULL))
  Argument names in docs not in code:
    conf.level conf.args
Package suggested but not available for checking: ‘hdf5r’
Note: found 9 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   7.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs        8.5Mb
    shiny_app   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘org.Hs.eg.db’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bayestestR’ ‘correlation’ ‘datawizard’ ‘effectsize’ ‘modelbased’
  ‘parameters’ ‘performance’ ‘report’ ‘see’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1409 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’ ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘econet.tex’ using tex
Error: processing vignette 'econet.tex' failed with diagnostics:
Running 'texi2dvi' on 'econet.tex' failed.
LaTeX errors:
! LaTeX Error: File `orcidlink.sty' not found.

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 77.4Mb
  sub-directories of 1Mb or more:
    libs  76.8Mb
GNU make is a SystemRequirements.
Note: found 7 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown
Warning: Removed 12 rows containing missing values (geom_point).
Warning: Removed 12 rows containing missing values (geom_label).
! Missing endcsname inserted.
<to be read again> 
                   unhbox 
l.293 \includegraphics{./images/Figure_1.png}

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
installed size is 130.2Mb
  sub-directories of 1Mb or more:
    libs  130.0Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 58.1Mb
  sub-directories of 1Mb or more:
    libs  56.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 50 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  15.3Mb
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Note: found 9451 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘sp’ ‘testthat’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    libs   2.1Mb
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    java   1.3Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMMAgeo’ ‘limSolve’ ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘matrixStats’
  All declared Imports should be used.
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.2Mb
Note: found 595 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
'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   6.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’ ‘tidyquant’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Running ‘testthat.R’ [26s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_helper_blocksize.R:34'): blockSize reports block size in row-col order ──
  Error: [writeRaster] invalid driver
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_helper_blocksize.R:34:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─terra::writeRaster(...) at test_helper_blocksize.R:35:4
   4. └─terra::writeRaster(...)
   5.   └─terra (local) .local(x, filename, ...)
   6.     └─terra:::messages(x, "writeRaster")
   7.       └─terra:::error(f, x@ptr$getError())
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 463 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    exiftool  14.0Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/expss.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
! LaTeX Error: File `orcidlink.sty' not found.

! Emergency stop.
<read *> 

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.0Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1430 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     2.9Mb
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    libs  47.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs  30.9Mb
Package suggested but not available for checking: ‘coxKM’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
Package suggested but not available for checking: ‘NNLM’
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   4.9Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘fst’ ‘kit’ ‘magrittr’ ‘matrixStats’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   6.7Mb
Unexported objects imported by ':::' calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Note: found 75 marked UTF-8 strings
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.1/fdaPDE.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.3Mb
Note: found 76 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 43825 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nflreadr’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       2.2Mb
    extdata   2.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    lib   11.2Mb
    libs  19.8Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Running ‘testthat.R’ [27s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(fitHeavyTail)
  > 
  > test_check("fitHeavyTail")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fit_mvst.R:43'): default mode works ──────────────────────────
  ...[] not equal to ...[].
  Component "num_iterations": Mean relative difference: 0.002739726
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory