installed size is 15.2Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  11.1Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.5Mb
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Undeclared packages ‘MCMCpack’, ‘bayesm’, ‘msm’ in Rd xrefs
File ‘MCMChybridGP/libs/MCMChybridGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘coda’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘grDevices’ ‘httr’
  ‘knitr’ ‘openssl’ ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’
  ‘spelling’ ‘testthat’ ‘utils’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.2Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  27.9Mb
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘patchwork’ ‘tidyverse’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
Undeclared packages ‘reshape’, ‘simba’, ‘labdsv’, ‘Hmisc’, ‘untb’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘adegenet’ ‘geosphere’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  19.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   6.2Mb
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
installed size is 112.0Mb
  sub-directories of 1Mb or more:
    libs  111.3Mb
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘Rgraphviz’ ‘fastAdaboost’ ‘graph’ ‘kernlab’ ‘klaR’
  ‘knitr’ ‘randomForest’ ‘reshape2’ ‘rpart’ ‘tools’
  All declared Imports should be used.
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘pacman’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared packages ‘metasens’, ‘robumeta’ in Rd xrefs
installed size is 110.5Mb
  sub-directories of 1Mb or more:
    libs  110.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.2Mb
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘R2WinBUGS’ in Rd xrefs
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    5.4Mb
    libs  20.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Undeclared packages ‘hoa’, ‘evir’ in Rd xrefs
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
File ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.0Mb
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.8Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Undeclared packages ‘micEconAids’, ‘micEconSNQP’ in Rd xrefs
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GenomicAlignments’ ‘R.utils’ ‘data.table’ ‘magrittr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘config’ ‘desc’ ‘dplyr’ ‘glue’ ‘withr’
  All declared Imports should be used.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    lib    8.6Mb
    libs   3.7Mb
Namespaces in Imports field not imported from:
  ‘AzureAuth’ ‘R6’ ‘curl’ ‘jsonlite’ ‘vctrs’
  All declared Imports should be used.
Undeclared package ‘riskRegression’ in Rd xrefs
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
installed size is 119.0Mb
  sub-directories of 1Mb or more:
    libs  118.4Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   6.4Mb
Undeclared package ‘scatterplot3d’ in Rd xrefs
Undeclared packages ‘pspline’, ‘lme4’ in Rd xrefs
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Undeclared package ‘quantmod’ in Rd xrefs
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘rms’, ‘Hmisc’, ‘genefilter’ in Rd xrefs
Undeclared packages ‘genefilter’, ‘MKmisc’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘MASS:::lda.default’ ‘MASS:::qda.default’
  ‘e1071:::naiveBayes.default’ ‘e1071:::svm.default’
  ‘randomForest:::randomForest.default’
  See the note in ?`:::` about the use of this operator.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlogitBMA/libs/mlogitBMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 316.1Mb
  sub-directories of 1Mb or more:
    libs  315.6Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Undeclared packages ‘lme4’, ‘rstanarm’, ‘dplyr’ in Rd xrefs
Namespace in Imports field not imported from: ‘parsnip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Undeclared package ‘roxygen2’ in Rd xrefs
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   4.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Undeclared package ‘seewave’ in Rd xrefs
Namespace in Imports field not imported from: ‘here’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ztable’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.2Mb
File ‘morse/libs/morse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘international-mortality-tables-overview.Rmd’ using rmarkdown
Quitting from lines 235-237 (international-mortality-tables-overview.Rmd) 
Error: processing vignette 'international-mortality-tables-overview.Rmd' failed with diagnostics:
could not find function "whittaker"
--- failed re-building ‘international-mortality-tables-overview.Rmd’

--- re-building ‘using-the-mortalityTables-package.Rmd’ using rmarkdown
--- finished re-building ‘using-the-mortalityTables-package.Rmd’

SUMMARY: processing the following file failed:
  ‘international-mortality-tables-overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggformula’ ‘magrittr’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggridges’ ‘ggstance’
  All declared Imports should be used.
Undeclared package ‘cubature’ in Rd xrefs
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
Undeclared package ‘graphlayouts’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
Package suggested but not available for checking: ‘CGHcall’
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 76.0Mb
  sub-directories of 1Mb or more:
    libs  75.6Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.8Mb
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘speedglm’ in Rd xrefs
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.0Mb
File ‘msda/libs/msda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   4.0Mb
    libs   3.6Mb
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  15.1Mb
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shape’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MultiCNVDetect/libs/MultiCNVDetect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    libs  57.0Mb
installed size is 115.3Mb
  sub-directories of 1Mb or more:
    doc     5.9Mb
    libs  108.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
  ‘pls’ ‘robustbase’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Undeclared packages ‘AICcmodavg’, ‘bbmle’, ‘glmulti’, ‘arm’, ‘wgeesel’, ‘ape’, ‘bestglm’, ‘leaps’, ‘glmmTMB’, ‘brglm’, ‘quantreg’, ‘maxlike’, ‘RMark’ in Rd xrefs
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvcluster/libs/mvcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘dosresmeta’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘mvMORPH’ in Rd xrefs
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    22.6Mb
    models   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
Undeclared packages ‘sSeq’, ‘PoiClaClu’ in Rd xrefs
Package unavailable to check Rd xrefs: ‘sSeq’
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NBPSeq/libs/NBPSeq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
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   5.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘downloader’ ‘jsonlite’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   6.7Mb
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.6Mb
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘CoDiNA’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘networkTomography/libs/networkTomography.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.8Mb
    classic-bugs   1.6Mb
    include        5.9Mb
    libs          15.5Mb
Undeclared packages ‘cshapes’, ‘mapdata’ in Rd xrefs
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  24.8Mb
Package in Depends field not imported from: ‘proto’
  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:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    examples   5.8Mb
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘multicool’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘s2’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Undeclared packages ‘quadprog’, ‘bvls’ in Rd xrefs
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘norm2/libs/norm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘bipartite’ in Rd xrefs
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘CAMAN’ ‘Hmisc’ ‘latexpdf’ ‘spatstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
Undeclared packages ‘logspline’, ‘ks’ in Rd xrefs
File ‘npst/libs/npst.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  17.5Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Undeclared packages ‘ensurer’, ‘validate’ in Rd xrefs
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.4Mb
    libs   3.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
installed size is 87.0Mb
  sub-directories of 1Mb or more:
    libs  86.5Mb
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
Namespaces in Imports field not imported from:
  ‘TCGAbiolinks’ ‘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.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.7Mb
File ‘onemap/libs/onemap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘miniUI’ ‘text2vec’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   5.4Mb
installed size is 211.5Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    libs    201.2Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
Namespaces in Imports field not imported from:
  ‘formattable’ ‘rintrojs’ ‘shinyBS’ ‘shinyFeedback’ ‘shinyWidgets’
  ‘shinycssloaders’ ‘shinydashboard’ ‘shinydashboardPlus’ ‘shinyjs’
  ‘shinythemes’ ‘splines’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      5.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.3Mb
Undeclared packages ‘alabama’, ‘cccp’, ‘nloptr’ in Rd xrefs
Running ‘exporting-methods.R’
  Running ‘testthat.R’ [43s/109s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘splines’
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
File ‘ordinalpattern/libs/ordinalpattern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
Undeclared package ‘microplot’ in Rd xrefs
Undeclared package ‘orloca.es’ in Rd xrefs
File ‘ORMDR/libs/ORMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
Undeclared package ‘maxmatching’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   6.0Mb
File ‘osmgeosample/libs/osmgeosample.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
Undeclared package ‘adegenet’ in Rd xrefs
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
Undeclared package ‘packClassic’ in Rd xrefs
Undeclared package ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespace in Imports field not imported from: ‘optparse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Undeclared package ‘analogue’ in Rd xrefs
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘trend’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
File ‘PAMA/libs/PAMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘rstudioapi’
  All declared Imports should be used.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs  49.9Mb
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘geoR’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survey’
  All declared Imports should be used.
Undeclared package ‘Familias’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tibble’
  All declared Imports should be used.
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Undeclared packages ‘glmnet’, ‘rstan’, ‘rstanarm’, ‘discrim’, ‘devtools’, ‘broom’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
Undeclared package ‘pathfindR’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘gplots’ ‘grid’ ‘jetset’ ‘magic’
  ‘msgps’ ‘splines’ ‘stats4’ ‘survival’
  All declared Imports should be used.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    lib  10.0Mb
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
Undeclared packages ‘tibble’, ‘data.table’ in Rd xrefs
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.0Mb
Undeclared packages ‘combinat’, ‘unifDAG’ in Rd xrefs
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
Undeclared package ‘spatstat.core’ in Rd xrefs
installed size is 134.7Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  131.1Mb
File ‘PCICt/libs/PCICt.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.1Mb
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘sm’, ‘spdep’ in Rd xrefs
File ‘PDFEstimator/libs/PDFEstimator.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘mlbench’, ‘foreach’, ‘ICEbox’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pedigree/libs/pedigree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘Hmisc’, ‘vcd’, ‘VecStatGraphs2D’, ‘mvtsplot’, ‘matrixStats’, ‘RandomFields’, ‘automap’, ‘spsann’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘dvir’ ‘ibdsim2’ ‘paramlink2’ ‘pedbuildr’ ‘segregatr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
File ‘perccal/libs/perccal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘timeSeries’, ‘tseries’, ‘car’, ‘gplots’ in Rd xrefs
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘classInt’, ‘PMCMR’, ‘agricolae’, ‘plotrix’, ‘AICcmodavg’ in Rd xrefs
File ‘pGMGM/libs/pGMGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    application   5.0Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘shinyWidgets’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    help   1.2Mb
    libs   4.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.5Mb
Undeclared package ‘phase1RMD’ in Rd xrefs
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
File ‘pheno/libs/pheno.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
Undeclared package ‘photobiologyLEDs’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   1.1Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
File ‘phyloland/libs/phyloland.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘future’, ‘geiger’, ‘caper’ in Rd xrefs
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘PhyloMeasures/libs/PhyloMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘picante’ in Rd xrefs
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  11.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘urltools’
  All declared Imports should be used.
Undeclared packages ‘pkgdown’, ‘htmlwidgets’ in Rd xrefs
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
File ‘plgp/libs/plgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘patchwork’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘gridExtra’
  All declared Imports should be used.
File ‘png/libs/png.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘plogr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
Undeclared package ‘ISOcodes’ in Rd xrefs
File ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
Undeclared package ‘flexmix’ in Rd xrefs
File ‘poLCA/libs/poLCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
    libs      3.4Mb
Undeclared package ‘BSgenome’ in Rd xrefs
Namespace in Imports field not imported from: ‘regtools’
  All declared Imports should be used.
installed size is 51.3Mb
  sub-directories of 1Mb or more:
    libs  51.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Undeclared package ‘ecodist’ in Rd xrefs
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Undeclared packages ‘rags2ridges’, ‘ragt2ridges’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Namespace in Imports field not imported from: ‘bslib’
  All declared Imports should be used.
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.
Undeclared packages ‘rstan’, ‘R2WinBUGS’, ‘R2jags’, ‘R2OpenBUGS’, ‘nimble’, ‘rjags’, ‘jagsUI’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Undeclared package ‘advclust’ in Rd xrefs
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.cache’ ‘docopt’ ‘here’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘adabag’ ‘colourpicker’ ‘e1071’ ‘flexdashboard’ ‘glmnet’
  ‘kknn’ ‘neuralnet’ ‘plyr’ ‘randomForest’ ‘rattle’ ‘rpart’ ‘shinyAce’
  ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’ ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘pkgdown’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    shinyApp   5.0Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  15.0Mb
Namespace in Imports field not imported from: ‘exactextractr’
  All declared Imports should be used.
Undeclared packages ‘ipflasso’, ‘mvtnorm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘rio’ ‘shiny’ ‘shinyjs’ ‘utils’ ‘webp’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      5.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.6Mb
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘optimx’ ‘tidyverse’
  All declared Imports should be used.
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
Undeclared packages ‘binom’, ‘PropCIs’, ‘BlakerCI’, ‘prevalence’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.8Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'proDA', 'STRINGdb'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.5Mb
Undeclared package ‘entropy’ in Rd xrefs
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    libs  38.9Mb
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    doc        4.0Mb
    examples   2.6Mb
installed size is 49.8Mb
  sub-directories of 1Mb or more:
    libs  49.4Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  32.2Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘mgcv’
  All declared Imports should be used.
Undeclared packages ‘vctrs’, ‘httr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Undeclared package ‘HURDAT’ in Rd xrefs
Unknown package ‘HURDAT’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
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          1.7Mb
    libs         2.8Mb
    staticdocs   3.4Mb
installed size is 54.5Mb
  sub-directories of 1Mb or more:
    libs  53.8Mb
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
installed size is 86.1Mb
  sub-directories of 1Mb or more:
    libs  85.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     41.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.6Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.2Mb
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.8Mb
Undeclared package ‘PredictABEL’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘collections’ ‘dplyr’
  All declared Imports should be used.
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: ‘batchelor’

Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
    libs   1.2Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
File ‘RAD/libs/RAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcompadre’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
Undeclared packages ‘longitudinal’, ‘gRbase’ in Rd xrefs
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets        9.7Mb
    super-tiny-icons   1.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.1Mb
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’ ‘xml2’
  All declared Imports should be used.
Found the following files/directories:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.pdf’
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   5.4Mb
Undeclared packages ‘spam’, ‘RandomFields’ in Rd xrefs
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  11.0Mb
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rasterKernelEstimates/libs/rasterKernelEstimates.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘crosstalk’ in Rd xrefs
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    libs   6.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 67.1Mb
  sub-directories of 1Mb or more:
    libs  66.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘deldir’ ‘lifecycle’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  32.4Mb
Undeclared packages ‘MCMCpack’, ‘gtools’ in Rd xrefs
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘PZ.bi’ ‘mu_sigma.nc’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   6.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
File ‘RCassandra/libs/RCassandra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Undeclared package ‘processx’ in Rd xrefs
Undeclared packages ‘BsMD’, ‘rsm’, ‘AlgDesign’, ‘lhs’ in Rd xrefs
Undeclared packages ‘car’, ‘leaps’, ‘latticeExtra’, ‘rgl’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Undeclared packages ‘e1071’, ‘RcmdrMisc’ in Rd xrefs
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
    po    2.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      1.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Undeclared package ‘RcppExamples’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    lib    4.8Mb
    libs   1.4Mb
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.5Mb
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 53.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      39.5Mb
    libs     11.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    lib       2.7Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      4.0Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    include        1.7Mb
    jsonexamples   3.8Mb
    libs          11.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SingleCellExperiment’ ‘mclust’
  All declared Imports should be used.
Undeclared package ‘Mercator’ in Rd xrefs
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  18.4Mb
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
File ‘Rdtq/libs/Rdtq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Undeclared packages ‘readMzXmlData’, ‘MALDIquantForeign’ in Rd xrefs
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘MALDIquantForeign’ in Rd xrefs
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Undeclared packages ‘tidyselect’, ‘vctrs’ in Rd xrefs
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
Undeclared package ‘rebus.unicode’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
Undeclared packages ‘workflows’, ‘hardhat’ in Rd xrefs
Package suggested but not available for checking: ‘opencv’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pkgload’ ‘processx’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’
  All declared Imports should be used.
Undeclared package ‘monomvn’ in Rd xrefs
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
Package which this enhances but not available for checking: ‘Rcplex’
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
File ‘rEMM/libs/rEMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    libs      3.4Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 53.1Mb
  sub-directories of 1Mb or more:
    libs  51.8Mb
Namespace in Imports field not imported from: ‘iCluster’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        3.4Mb
    pictures   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
Undeclared package ‘Matching’ in Rd xrefs
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.8Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Running examples in ‘rgho-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_gho_dimensions
> ### Title: Returns GHO Dimensions/Codes
> ### Aliases: get_gho_dimensions get_gho_codes man-gho print.gho
> 
> ### ** Examples
> 
> 
> get_gho_dimensions()
Error during request:
Server error: (503) Service Unavailable
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘a-intro.Rmd’ using rmarkdown
Quitting from lines 30-31 (a-intro.Rmd) 
Error: processing vignette 'a-intro.Rmd' failed with diagnostics:

--- failed re-building ‘a-intro.Rmd’

--- re-building ‘b-dimensions.Rmd’ using rmarkdown
Quitting from lines 21-22 (b-dimensions.Rmd) 
Error: processing vignette 'b-dimensions.Rmd' failed with diagnostics:

--- failed re-building ‘b-dimensions.Rmd’

--- re-building ‘c-codes-gho.Rmd’ using rmarkdown
Quitting from lines 21-22 (c-codes-gho.Rmd) 
Error: processing vignette 'c-codes-gho.Rmd' failed with diagnostics:

--- failed re-building ‘c-codes-gho.Rmd’

--- re-building ‘d-codes-country.Rmd’ using rmarkdown
Quitting from lines 21-28 (d-codes-country.Rmd) 
Error: processing vignette 'd-codes-country.Rmd' failed with diagnostics:

--- failed re-building ‘d-codes-country.Rmd’

--- re-building ‘e-details.Rmd’ using rmarkdown
--- finished re-building ‘e-details.Rmd’

SUMMARY: processing the following files failed:
  ‘a-intro.Rmd’ ‘b-dimensions.Rmd’ ‘c-codes-gho.Rmd’
  ‘d-codes-country.Rmd’

Error: Vignette re-building failed.
Execution halted
Undeclared packages ‘lpSolve’, ‘ROI’, ‘Rsymphony’ in Rd xrefs
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    fonts     1.5Mb
    libs      2.6Mb
    useNULL   1.9Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   9.6Mb
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’
File ‘RGtk2/libs/RGtk2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.3Mb
Undeclared packages ‘tseries’, ‘TSA’ in Rd xrefs
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Undeclared packages ‘dtw’, ‘fastcluster’, ‘Rtsne’ in Rd xrefs
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Undeclared package ‘utility’ in Rd xrefs
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  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.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
':::' calls which should be '::':
  ‘stats:::dexp’ ‘stats:::dgamma’ ‘stats:::dweibull’ ‘stats:::pexp’
  ‘stats:::pgamma’ ‘stats:::pweibull’ ‘stats:::qexp’ ‘stats:::qgamma’
  ‘stats:::qweibull’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rweibull’
  See the note in ?`:::` about the use of this operator.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
Found the following files/directories:
  ‘dipper.inp’ ‘mark001.inp’ ‘mark001.out’ ‘mark001.res’ ‘mark001.vcv’
  ‘mark002.inp’ ‘mark002.out’ ‘mark002.res’ ‘mark002.vcv’ ‘mark003.inp’
  ‘mark003.out’ ‘mark003.res’ ‘mark003.vcv’ ‘mark004.inp’ ‘mark004.out’
  ‘mark004.res’ ‘mark004.vcv’ ‘mark005.inp’ ‘mark005.out’ ‘mark005.res’
  ‘mark005.vcv’ ‘mark006.inp’ ‘mark006.out’ ‘mark006.res’ ‘mark006.vcv’
  ‘mark007.inp’ ‘mark007.out’ ‘mark007.res’ ‘mark007.vcv’ ‘mark008.inp’
  ‘mark008.out’ ‘mark008.res’ ‘mark008.vcv’ ‘mark009.inp’ ‘mark009.out’
  ‘mark009.res’ ‘mark009.vcv’ ‘mark010.inp’ ‘mark010.out’ ‘mark010.res’
  ‘mark010.vcv’ ‘mark010V.tmp’ ‘mark010X.tmp’ ‘mark010Y.tmp’
  ‘mark011.inp’ ‘mark011.out’ ‘mark011.res’ ‘mark011.vcv’ ‘mark012.inp’
  ‘mark012.out’ ‘mark012.res’ ‘mark012.vcv’ ‘mark013.inp’ ‘mark013.out’
  ‘mark013.res’ ‘mark013.vcv’
installed size is 66.6Mb
  sub-directories of 1Mb or more:
    libs  65.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs       1.2Mb
    minizinc   3.4Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 55.1Mb
  sub-directories of 1Mb or more:
    libs  54.5Mb
Undeclared package ‘fortunes’ in Rd xrefs
Found the following significant warnings:
  lex.yy.c:1606:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration]
See ‘/data/gannet/ripley/R/packages/tests-clang/rmumps.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
File ‘RMVL/libs/RMVL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Undeclared packages ‘fossil’, ‘raster’ in Rd xrefs
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 89.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     87.5Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
Package suggested but not available for checking: ‘affydata’
Undeclared package ‘distrEx’ in Rd xrefs
Undeclared package ‘ROptEst’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘bridgesampling’ ‘callr’ ‘extraDistr’ ‘psych’ ‘runjags’
  All declared Imports should be used.
Undeclared package ‘svdvisual’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘robustgam/libs/robustgam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
Undeclared packages ‘mvtnorm’, ‘scatterplot3d’, ‘HH’ in Rd xrefs
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
File ‘Rook/libs/Rook.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘readroper’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘diptest’ ‘methods’ ‘viridis’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.5Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
Undeclared package ‘scalreg’ in Rd xrefs
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsae/libs/rsae.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSclient/libs/RSclient.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘keras’, ‘tensorflow’, ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘labelled’
  All declared Imports should be used.
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2150:17: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarations]
  oc.c:47:33: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  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 call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  14.4Mb
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  kr_pat_scan.cpp:1472:12: warning: function 'yyinput' is not needed and will not be emitted [-Wunneeded-internal-declaration]
See ‘/data/gannet/ripley/R/packages/tests-clang/RSNNS.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  42.8Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘knitr’
  All declared Imports should be used.
installed size is 201.4Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  194.7Mb
Undeclared packages ‘gamm4’, ‘shiny’, ‘biglm’ in Rd xrefs
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
installed size is 199.2Mb
  sub-directories of 1Mb or more:
    lib    34.5Mb
    libs  161.9Mb
Undeclared packages ‘coda’, ‘rstanarm’ in Rd xrefs
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Undeclared package ‘flexsurv’ in Rd xrefs
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
Found the following significant warnings:
  devSVG.c:704:11: warning: expression which evaluates to zero treated as a null pointer constant of type 'int *' [-Wnon-literal-null-conversion]
See ‘/data/gannet/ripley/R/packages/tests-clang/RSvgDevice.Rcheck/00install.out’ for details.
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  devSVG.c:1812:41: warning: expression which evaluates to zero treated as a null pointer constant of type 'int *' [-Wnon-literal-null-conversion]
See ‘/data/gannet/ripley/R/packages/tests-clang/RSVGTipsDevice.Rcheck/00install.out’ for details.
File ‘RSVGTipsDevice/libs/RSVGTipsDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘lpSolve’, ‘Rglpk’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R           1.2Mb
    bootstrap   1.6Mb
    data        2.2Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    rmarkdown   5.1Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.1Mb
    projects   2.8Mb
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  17.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rmarkdown’ ‘table1’
  All declared Imports should be used.
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.6Mb
installed size is 50.1Mb
  sub-directories of 1Mb or more:
    libs  49.3Mb
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs     49.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
    test   4.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    libs  52.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs    7.4Mb
    yacas   1.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs    7.9Mb
    yacas   1.6Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs     31.2Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Undeclared packages ‘magrittr’, ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs  14.2Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  22.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.3Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sapa/libs/sapa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    bin  42.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.2Mb
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAVE/libs/SAVE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbioPN/libs/sbioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   4.1Mb
File ‘SBSA/libs/SBSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘methods’
  All declared Imports should be used.
Undeclared packages ‘Iso’, ‘scam’, ‘gam’ in Rd xrefs
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sde/libs/sde.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Undeclared package ‘randomNames’ in Rd xrefs
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
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
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
File ‘SearchTrees/libs/SearchTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  16.0Mb
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rsbml’
Undeclared packages ‘EDNE.EQ’, ‘T2EQ’ in Rd xrefs
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
Undeclared package ‘SemNetCleaner’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Undeclared packages ‘NetworkToolbox’, ‘SemNetCleaner’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.8Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs    15.7Mb
    models   1.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘airway’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  13.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Imports includes 41 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   7.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Namespace in Imports field not imported from: ‘geometries’
  All declared Imports should be used.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    doc      2.3Mb
    libs     9.0Mb
    sqlite   1.5Mb
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    www  16.5Mb
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘purrr’ ‘shinyBS’ ‘shinydashboard’
  ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    shinyApp  21.4Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    www   9.0Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'

Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Packages unavailable to check Rd xrefs: ‘TFBSTools’, ‘motifmatchr’, ‘chromVAR’
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared packages ‘ade4’, ‘labdsv’, ‘sp’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
Undeclared packages ‘GenOrd’, ‘PoisNor’ in Rd xrefs
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘future’ ‘magrittr’ ‘purrr’ ‘rlang’ ‘utils’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  10.2Mb
Undeclared packages ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’ in Rd xrefs
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘jsonlite’ ‘readr’ ‘shinycssloaders’ ‘tibble’
  All declared Imports should be used.
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.2Mb
Namespaces in Imports field not imported from:
  ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  19.4Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   7.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CompQuadForm’ ‘Hmisc’ ‘boot’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Undeclared package ‘RcmdrPlugin.SLC’ in Rd xrefs
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Undeclared packages ‘InformationValue’, ‘ggthemes’ in Rd xrefs
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   1.3Mb
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.7Mb
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rgeos’
  All declared Imports should be used.
Undeclared package ‘RcppArmadillo’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.6Mb
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.2Mb
    libs   6.6Mb
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘testthat’ in Rd xrefs
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.1Mb
Namespaces in Imports field not imported from:
  ‘gtools’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.3Mb
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘colorSpec’ in Rd xrefs
Undeclared package ‘rebus.base’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Require’
  All declared Imports should be used.
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs  34.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.3Mb
Undeclared packages ‘splancs’, ‘spatstat.data’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Undeclared package ‘sparsebn’ in Rd xrefs
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseSEM/libs/sparseSEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    help   1.7Mb
    libs   1.2Mb
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridisLite’
  All declared Imports should be used.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  20.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘ggplot2’ ‘parallel’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.1Mb
    libs   1.1Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   9.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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   1.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.1Mb
    etc   1.4Mb
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xcms’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rcytoscapejs’

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘specmine.datasets’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘pdftools’
  All declared Imports should be used.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Undeclared packages ‘reshape2’, ‘sampling’, ‘dplyr’ in Rd xrefs
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      2.9Mb
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
Namespace in Imports field not imported from: ‘batchtools’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘car’ ‘knitr’ ‘lmtest’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 49.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  47.6Mb
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’ ‘spatstat.linnet’ ‘spatstat.sparse’
  ‘spatstat.utils’ ‘testthat’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Undeclared packages ‘RColorBrewer’, ‘colorspace’ in Rd xrefs
Namespace in Imports field not imported from: ‘sessioninfo’
  All declared Imports should be used.
installed size is 76.6Mb
  sub-directories of 1Mb or more:
    libs  76.2Mb
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
Undeclared packages ‘pryr’, ‘functional’, ‘dplyr’, ‘ks’, ‘purrr’, ‘data.table’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘workflowsets’ ‘yardstick’
  All declared Imports should be used.
Undeclared packages ‘h2o’, ‘SuperLearner’ in Rd xrefs
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include  10.7Mb
    lib       3.0Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyselect’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    4.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Undeclared package ‘HDoutliers’ in Rd xrefs
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   9.7Mb
Namespace in Imports field not imported from: ‘dbscan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘utf8’
  All declared Imports should be used.
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc  10.9Mb
Namespaces in Imports field not imported from:
  ‘psych’ ‘referenceIntervals’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘backports’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
Undeclared package ‘truncdist’ in Rd xrefs
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    libs   1.6Mb
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 138.1Mb
  sub-directories of 1Mb or more:
    libs  137.2Mb
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘readr’ ‘rlang’ ‘survival’ ‘tidyverse’ ‘utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.3Mb
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Undeclared package ‘survJamda’ in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  12.6Mb
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   7.1Mb
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
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.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Undeclared package ‘mlbench’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.0Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘duckdb’ ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jsonlite’ ‘knitr’ ‘lazyeval’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘taxa’
  All declared Imports should be used.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  11.2Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  27.8Mb
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘survivalROC’ in Rd xrefs
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    apps   3.2Mb
    libs  10.0Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    libs      1.6Mb
    telemac   1.0Mb
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    libs  35.9Mb
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Undeclared packages ‘h2o’, ‘eha’, ‘mfx’, ‘betareg’, ‘brglm’, ‘censReg’, ‘ergm’, ‘latentnet’, ‘fGarch’, ‘gee’, ‘geepack’, ‘gmm’, ‘robustbase’, ‘gnm’, ‘pscl’, ‘robust’, ‘sna’, ‘lqmm’, ‘rms’, ‘erer’, ‘mhurdle’, ‘oglmx’, ‘panelAR’, ‘pglm’, ‘relevent’, ‘quantreg’, ‘spatialreg’, ‘sampleSelection’, ‘RSiena’, ‘simex’, ‘tergm’, ‘survey’, ‘systemfit’, ‘metaSEM’ in Rd xrefs
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   4.3Mb
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.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Undeclared packages ‘tm’, ‘textreadr’ in Rd xrefs
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘proxy’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘purrr’ ‘readr’
  All declared Imports should be used.
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Undeclared packages ‘fastDummies’, ‘sjmisc’ in Rd xrefs
Undeclared packages ‘tidyfst’, ‘tidyr’, ‘fastDummies’ in Rd xrefs
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Evomorph’ ‘cowplot’ ‘factoextra’ ‘gridExtra’ ‘lme4’ ‘lsr’ ‘plotly’
  ‘png’ ‘shapes’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘modeldata’ ‘workflowsets’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘janitor’
  All declared Imports should be used.
installed size is 52.8Mb
  sub-directories of 1Mb or more:
    libs  51.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dtplyr’ ‘googledrive’ ‘googlesheets4’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 49.7Mb
  sub-directories of 1Mb or more:
    libs     9.6Mb
    tiledb  38.1Mb
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘base64enc’
  All declared Imports should be used.
Undeclared package ‘modeltools’ in Rd xrefs
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    examples  13.5Mb
    include    3.0Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Undeclared packages ‘tm.plugin.dc’, ‘readtext’, ‘graph’, ‘tau’, ‘tokenizers’ in Rd xrefs
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘PROJ’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fs’ ‘stringr’ ‘torch’ ‘torchvision’ ‘zip’
  All declared Imports should be used.
installed size is 113.7Mb
  sub-directories of 1Mb or more:
    R       4.5Mb
    help    1.4Mb
    libs  107.3Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
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
Undeclared packages ‘g.data’, ‘filehash’ in Rd xrefs
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: ‘neuralnet’
  All declared Imports should be used.
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘boot’ ‘chron’ ‘randtoolbox’
  All declared Imports should be used.
installed size is 124.1Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    libs  119.2Mb
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gsrsb’
  All declared Imports should be used.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘countrycode’ ‘haven’ ‘readstata13’ ‘stringr’ ‘tibble’ ‘tidyr’
  All declared Imports should be used.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ez’ ‘forcats’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Undeclared package ‘tempdisagg’ in Rd xrefs
Undeclared packages ‘fpc’, ‘clValid’, ‘clv’ in Rd xrefs
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘TSSQLite’, ‘TSMySQL’, ‘TSPostgreSQL’ in Rd xrefs
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.5Mb
Undeclared package ‘rugarch’ in Rd xrefs
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.4Mb
Undeclared package ‘tseries’ in Rd xrefs
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
Undeclared packages ‘multcomp’, ‘agricolae’ in Rd xrefs
Undeclared package ‘randomForest’ in Rd xrefs
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘xgboost’ in Rd xrefs
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.2Mb
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  50.1Mb
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc        1.6Mb
    shinyapp   3.4Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       19.4Mb
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    libs      2.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   4.1Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs  26.5Mb
Namespaces in Imports field not imported from:
  ‘lavaan’ ‘lifecycle’ ‘patchwork’ ‘ragg’ ‘scales’ ‘simstandard’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   6.4Mb
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.
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
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.
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘rlang’ ‘tidyverse’
  All declared Imports should be used.
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘candisc’ in Rd xrefs
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘coin’, ‘Hmisc’ in Rd xrefs
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
Undeclared packages ‘ade4’, ‘cclust’, ‘bipartite’, ‘labdsv’, ‘ellipse’, ‘vegan3d’, ‘coda’, ‘maptools’, ‘ape’, ‘picante’ in Rd xrefs
Undeclared packages ‘mclust’, ‘e1071’ in Rd xrefs
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   2.8Mb
Namespaces in Imports field not imported from:
  ‘plotrix’ ‘sp’ ‘viridis’
  All declared Imports should be used.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Undeclared packages ‘foreach’, ‘copula’ in Rd xrefs
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘vioplot’, ‘beanplot’, ‘beeswarm’, ‘parviol’ in Rd xrefs
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   6.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.0Mb
Namespace in Imports field not imported from: ‘parcats’
  All declared Imports should be used.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘colorspace’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glue’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 74.3Mb
  sub-directories of 1Mb or more:
    libs  73.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Calculate_WACC_in_R.Rmd’ using rmarkdown
Quitting from lines 30-36 (Calculate_WACC_in_R.Rmd) 
Error: processing vignette 'Calculate_WACC_in_R.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building ‘Calculate_WACC_in_R.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 75.8Mb
  sub-directories of 1Mb or more:
    libs  74.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘jsonlite’
  ‘leaflet.extras’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘sp’ ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lemon’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’

--- re-building ‘united_nations.Rmd’ using rmarkdown

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

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
Can't join on `x$a2` x `y$a2` because of incompatible types.
ℹ `x$a2` is of type <logical>>.
ℹ `y$a2` is of type <character>>.
--- failed re-building ‘united_nations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Undeclared package ‘WikipediR’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Undeclared packages ‘wpp2010’, ‘wpp2012’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.4Mb
    extdata   2.4Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.1Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/x13binary.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    bin   5.7Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      1.8Mb
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/cairoDevice.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘future’ ‘iterators’ ‘readr’
  All declared Imports should be used.
Compilation used the following non-portable flag(s):
  ‘-Werror=implicit-function-declaration)’
Found the following files/directories:
  ‘emeScheme’
Found the following files/directories:
  ‘schlegel’
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building ‘pritikin-schmidt.Rnw’ using knitr

Quitting from lines 858-929 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
The job for model 'container' exited abnormally with the error message: User interrupt
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘methods’ ‘reshape2’
  All declared Imports should be used.
Found the following files/directories:
  ‘pkgbuild’
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.2/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.2/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.2/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/lolog.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Running ‘exporting-methods.R’
  Running ‘testthat.R’ [55s/131s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1612 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘veryImportantPackage’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/RDieHarder.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘4.2’
Running ‘testthat.R’ [151s/177s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskmetric)
  > 
  > options(repos = "fake-cran.fake-r-project.org")
  > 
  > test_check("riskmetric")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • snapshots appear to be failing due to random order of pkg_ref fields (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_pkg_ref.R:31:3): pkg_ref infers source when not explicitly provided ──
  `ref3` has class 'pkg_install'/'pkg_ref'/'environment', not 'pkg_bioc_remote'/'pkg_remote'/'pkg_ref'/'environment'.
  ── Failure (test_pkg_ref.R:32:3): pkg_ref infers source when not explicitly provided ──
  ref3$source (`actual`) not equal to "pkg_bioc_remote" (`expected`).
  
  `actual`:   "pkg_install"    
  `expected`: "pkg_bioc_remote"
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 45 ]
  Error: Test failures
  Execution halted
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  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 call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/RVowpalWabbit.Rcheck/00install.out’ for details.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Found the following files/directories:
  ‘devtools’
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extdata   8.3Mb
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.1Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    gdal   2.2Mb
    libs  43.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Running examples in 'arealDB-Ex.R' failed
The error most likely occurred in:

> ### Name: makeExampleDB
> ### Title: Build an example database
> ### Aliases: makeExampleDB
> 
> ### ** Examples
> 
> # to merely register a set of files
> makeExampleDB(until = "regTable")
I have created a new project directory.
  -> please run 'setVariables()' to create a translation table for territories.
please type in the path to the local folder where the licence is stored: 
Error: Cannot open file for writing:
* 'D:\temp\RtmpO66tUq\newDB\inv_dataseries.csv'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.1Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    libs  18.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.1Mb
    misc   2.1Mb
Found the following significant warnings:
  wmm.c:428:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int)'} [-Wincompatible-pointer-types]
  wmm.c:429:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int,  int)'} [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/audio.Rcheck/00install.out' for details.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2021-07-31 r80687) -- "Unsuffered Consequences"
Copyright (C) 2021 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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BALD.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.1Mb
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Package suggested but not available for checking: 'doMC'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running examples in 'beautier-Ex.R' failed
The error most likely occurred in:

> ### Name: check_empty_beautier_folder
> ### Title: Check there are no files in the default beautier folder
> ### Aliases: check_empty_beautier_folder
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
Error in check_empty_beautier_folder() : Files found in beautier folder. 
beautier_folder: C:\Users\CRAN\AppData\Local/beautier/beautier/Cache 
length(list.files(beautier_folder))): 3 
head(list.files(beautier_folder)): C:\Users\CRAN\AppData\Local/beautier/beautier/Cache/file13670ff35c02,C:\Users\CRAN\AppData\Local/beautier/beautier/Cache/file178c45757dd,C:\Users\CRAN\AppData\Local/beautier/beautier/Cache/fileb9f87bd32678
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.9Mb
    libs   1.2Mb
installed size is 143.0Mb
  sub-directories of 1Mb or more:
    include  142.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BioMedR.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BioVenn.Rcheck/00install.out' for details.
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.
Error(s) in re-building vignettes:
--- re-building 'bkmrhat-vignette.Rmd' using knitr
For guided examples, go to 'https://jenfb.github.io/bkmr/overview.html'
Loading required package: coda
Diagnostics and parallel chain functioning for Bayesian kernel machine regression
Quitting from lines 41-54 (bkmrhat-vignette.Rmd) 
Error: processing vignette 'bkmrhat-vignette.Rmd' failed with diagnostics:
Initialization of plan() failed, because the test future used for validation failed. The reason was: Package 'future' is not installed on worker (r_version: R Under development (unstable) (2021-07-31 r80687); platform: x86_64-w64-mingw32 (64-bit); os: Windows Server 2008 x64 build 6003, Service Pack 2; hostname: CRANWIN)
--- failed re-building 'bkmrhat-vignette.Rmd'

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

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

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  URL 'https://www-users.york.ac.uk/~mb55/datasets/darbela.dct': status was 'SSL connect error'
Error in file(con, "r") : 
  cannot open the connection to 'https://www-users.york.ac.uk/~mb55/datasets/darbela.dct'
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BonEV.Rcheck/00install.out' for details.
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
    lib      28.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BRugs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/Brundle.Rcheck/00install.out' for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    7.7Mb
    libs   6.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    fonts   2.4Mb
    lib     3.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  w32-backend.c:24:5: warning: initialization of 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/Cairo.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    pictures   3.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    doc  37.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Running examples in 'cbsodataR-Ex.R' failed
The error most likely occurred in:

> ### Name: cbs_get_catalogs
> ### Title: Retrieves the possible catalog values that can be used for
> ###   retrieving data
> ### Aliases: cbs_get_catalogs
> 
> ### ** Examples
> 
> catalogs <- cbs_get_catalogs()
Warning in open.connection(con, "rb") :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': status was 'SSL connect error'
Warning: Failing: http://opendata.cbs.nl/ODataCatalog/Tables?$format=json
Retrying...
Warning in open.connection(con, "rb") :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': status was 'SSL connect error'
Error in open.connection(con, "rb") : 
  cannot open the connection to 'http://opendata.cbs.nl/ODataCatalog/Tables?$format=json'
Calls: cbs_get_catalogs ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.1Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/cepreader.Rcheck/00install.out' for details.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/commonsMath.Rcheck/00install.out' for details.
Running examples in 'compstatr-Ex.R' failed
The error most likely occurred in:

> ### Name: cs_load_year
> ### Title: Create Year List Object
> ### Aliases: cs_load_year
> 
> ### ** Examples
> 
> # create temporary directory
> tmpdir <- tempdir()
> fs::dir_create(paste0(tmpdir,"/data/"))
> 
> # load sample files into temporary directory
> cs_example(path = paste0(tmpdir,"/data/"))
> 
> # prep sample files
> cs_prep_year(path = paste0(tmpdir,"/data/"))
> 
> # load sample files
> yearList17 <- cs_load_year(path = paste0(tmpdir,"/data/"))
> 
> # delete data
> fs::dir_delete(paste0(tmpdir,"/data/"))
Error: [EBUSY] Failed to remove 'D:/temp/RtmpWcyw3Q/data/april2017.csv': resource busy or locked
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.6Mb
Package suggested but not available for checking: 'ProData'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Running examples in 'crsra-Ex.R' failed
The error most likely occurred in:

> ### Name: crsra_import_course
> ### Title: Imports all the .csv files into one list consisting of all the
> ###   tables within the course.
> ### Aliases: crsra_import_course
> 
> ### ** Examples
> 
> zip_file = system.file("extdata", "fake_course_7051862327916.zip",
+ package = "crsra")
> bn = basename(zip_file)
> bn = sub("[.]zip$", "", bn)
> res = unzip(zip_file, exdir = tempdir(), overwrite = TRUE)
Error in unzip(zip_file, exdir = tempdir(), overwrite = TRUE) : 
  cannot open file 'D:/temp/RtmpoTuH7V/fake_course_7051862327916/programming_submission_part_grid_grading_statuses.csv': Invalid argument
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   5.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/curl.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    help   1.0Mb
    libs   1.2Mb
Package which this enhances but not available for checking: 'doMC'
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    deps  10.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    lib   8.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
Error(s) in re-building vignettes:
--- re-building 'datadigest.Rmd' using rmarkdown
pandoc.exe: Unknown extension: gfm_auto_identifiers
Error: processing vignette 'datadigest.Rmd' failed with diagnostics:
pandoc document conversion failed with error 7
--- failed re-building 'datadigest.Rmd'

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

Error: Vignette re-building failed.
Execution halted
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11563 (sockconn)
Execution halted
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.8Mb
    help   1.5Mb
    libs   1.1Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc           9.7Mb
    htmlwidgets   2.8Mb
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:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11324 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11324 (sockconn)
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    help   1.3Mb
    libs   1.1Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  15.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.2Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   2.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
Running 'testthat.R' [64s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  == Failed tests ================================================================
  -- Failure (test-news.R:34:3): update_news works -------------------------------
  `find_news(path = dir_loc)` did not throw an error.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 554 ]
  Error: Test failures
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    bin       3.2Mb
    extdata   1.7Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Title: Trim and Format Address Information
> ### Aliases: trim_address
> 
> ### ** Examples
> 
> addr_string <- " 2 Dept of Urology, Feinberg School of Medicine," 
> addr_string <- paste(addr_string, "Chicago, US; Dept of Mol Bio as well...")
> print(addr_string)
[1] " 2 Dept of Urology, Feinberg School of Medicine, Chicago, US; Dept of Mol Bio as well..."
> print(trim_address(addr = addr_string))
[1] "Dept of Urology, Feinberg School of Medicine, Chicago, US"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.58 0.56 485.24 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 ?) ========
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
Running examples in 'EIAdata-Ex.R' failed
The error most likely occurred in:

> ### Name: EIAdata-package
> ### Title: R wrapper for the US Energy Information Administration's (EIA's)
> ###   API.
> ### Aliases: EIAdata-package EIAdata
> ### Keywords: EIAdata
> 
> ### ** Examples
> 
> # The function wngsr will return a list object containing the time
> # the report was run, and the contents of the US EIA's Weekly
> # Natural Gas Storage Report.  The function has no arguments,
> # so simply run:
> 
> wngsr()
Warning in file(file, "rt") :
  URL 'https://ir.eia.gov/ngs/wngsr.csv': status was 'SSL connect error'
Error in file(file, "rt") : 
  cannot open the connection to 'http://ir.eia.gov/ngs/wngsr.csv'
Calls: wngsr -> <Anonymous> -> read.table -> file
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error(s) in re-building vignettes:
--- re-building 'estudy2-intro.Rmd' using rmarkdown
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.

Warning: CS.PA contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: G.MI contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: RSA.L download failed; trying again.
Quitting from lines 56-64 (estudy2-intro.Rmd) 
Error: processing vignette 'estudy2-intro.Rmd' failed with diagnostics:
Unable to import "RSA.L".
argument "conn" is missing, with no default
--- failed re-building 'estudy2-intro.Rmd'

SUMMARY: processing the following file failed:
  'estudy2-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(evaluator)
  > 
  > # ensure phantom.js is available on CI platforms
  > if (Sys.getenv("NOT_CRAN", "") != "" || Sys.getenv("CI", "") != "") {
  +   if (!shinytest::dependenciesInstalled()) shinytest:::installDependencies()
  +   message("Using phantom.js from ", shinytest:::find_phantom(), "\n")
  + }
  > 
  > test_check("evaluator")
  # Scenario model: openfair_tef_tc_diff_lm
  == Skipped tests ===============================================================
  * Not running MVA test - EVALUATOR_TEST_MVA not set (1)
  * On CRAN (1)
  * Shiny testing is awkward, consider moving to stand along pkg (1)
  * empty test (1)
  
  == Failed tests ================================================================
  -- Error (test-reports.R:19:1): (code run outside of `test_that()`) ------------
  Error: Cannot open file for writing:
  * 'D:\temp\RtmpCgcVFx\inputs\qualitative_scenarios.csv'
  Backtrace:
      x
   1. \-readr::write_csv(...) test-reports.R:19:0
   2.   \-readr::write_delim(...)
   3.     \-vroom::vroom_write(...)
   4.       \-vroom:::vroom_write_(...)
  
  [ FAIL 1 | WARN 1 | SKIP 4 | PASS 136 ]
  Error: Test failures
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    Rcgi      3.2Mb
    cgi-bin   3.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.5Mb
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.2Mb
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    4.0Mb
    libs   1.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: 'dggrids'
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.5Mb
    help   1.4Mb
    libs  12.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   1.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.4Mb
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(GBcurves)
  > 
  > test_check("GBcurves")
  == Failed tests ================================================================
  -- Failure (test_gb.R:23:3): Test function -------------------------------------
  nrow(df.out) > 0 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    doc      1.0Mb
    gdal     2.1Mb
    libs    44.8Mb
    proj     8.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      1.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R  10.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Running examples in 'ggguitar-Ex.R' failed
The error most likely occurred in:

> ### Name: select_chords
> ### Title: Select chords by criteria
> ### Aliases: select_chords
> 
> ### ** Examples
> 
> select_chords(chord_name = 'Major', string_5_fret = 3)
Warning: `filter_()` was deprecated in dplyr 0.7.0.
Please use `filter()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error in if (!is.null(value) && value != "") { : 
  missing value where TRUE/FALSE needed
Calls: select_chords -> narrow_chord
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.1Mb
    testdata   4.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs           13.7Mb
    test_data       2.0Mb
    vignette_data   1.1Mb
Package suggested but not available for checking: 'cplexAPI'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R   6.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error(s) in re-building vignettes:
--- re-building 'grob_layout.Rmd' using rmarkdown
--- finished re-building 'grob_layout.Rmd'

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

--- re-building 'grobblR.Rmd' using rmarkdown
Quitting from lines 260-278 (grobblR.Rmd) 
Error: processing vignette 'grobblR.Rmd' failed with diagnostics:
The object passed through grob_image() must either be a ggplot object, an existing URL to a .png image or an existing local file path to a .png image.
--- failed re-building 'grobblR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 168.9Mb
  sub-directories of 1Mb or more:
    R       1.2Mb
    java  166.3Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  == Failed tests ================================================================
  -- Failure (testall.R:22:3): test the haze -------------------------------------
  floor(h$haze * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 225, 224).
  1/1 mismatches
  [1] 224 - 225 == -1
  -- Failure (testall.R:23:3): test the haze -------------------------------------
  floor(h$A0 * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 710, 712).
  1/1 mismatches
  [1] 712 - 710 == 2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Running examples in 'horizon-Ex.R' failed
The error most likely occurred in:

> ### Name: horizonSearch
> ### Title: Horizon elevation angle from DEM RasterLayer
> ### Aliases: horizonSearch
> 
> ### ** Examples
> 
> r <- getData('alt', country='ALB')
trying URL 'https://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip'
Warning in utils::download.file(url = aurl, destfile = fn, method = "auto",  :
  URL 'https://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip': status was 'Couldn't connect to server'
Error in utils::download.file(url = aurl, destfile = fn, method = "auto",  : 
  cannot open URL 'https://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip'
Calls: getData -> .raster -> .download -> <Anonymous>
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
Running examples in 'httr-Ex.R' failed
The error most likely occurred in:

> ### Name: VERB
> ### Title: VERB a url.
> ### Aliases: VERB
> 
> ### ** Examples
> 
> r <- VERB(
+   "PROPFIND", "http://svn.r-project.org/R/tags/",
+   add_headers(depth = 1), verbose()
+ )
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [svn.r-project.org] Connection timed out after 10011 milliseconds
Calls: VERB ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
> model$output$fit
[1] 0.4515827
> model$output$gradient
x1 
 0 
> model$output$hessian
   x1
x1  8
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.27 0.42 7.83 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 ?) ========
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   6.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    dlib-19.20   8.9Mb
    libs         1.3Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs      7.8Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs   10.1Mb
    share  10.2Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "polygon",
             "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
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.
Running 'test-all.R' [3s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("iptools")
  Loading required package: iptools
  == Failed tests ================================================================
  -- Error (test-cidr-ops.R:5:3): asn table ops work -----------------------------
  Error: embedded nul in string: '1.1.148.0\021'
  Backtrace:
      x
   1. \-iptools::asn_table_to_trie(...) test-cidr-ops.R:5:2
   2.   \-stringi::stri_split_fixed(rip$cidr, "/", 2, simplify = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ]
  Error: Test failures
  Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11668 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11668 (sockconn)
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.2Mb
    data   1.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.2Mb
Error(s) in re-building vignettes:
--- re-building 'janitor.Rmd' using rmarkdown

Attaching package: 'janitor'

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

    chisq.test, fisher.test

pandoc.exe: Unknown extension: gfm_auto_identifiers
Error: processing vignette 'janitor.Rmd' failed with diagnostics:
pandoc document conversion failed with error 7
--- failed re-building 'janitor.Rmd'

--- re-building 'tabyls.Rmd' using rmarkdown

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

--- finished re-building 'tabyls.Rmd'

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

Error: Vignette re-building failed.
Execution halted
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs             1.1Mb
    shiny-landsepi   1.3Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.2Mb
Package unavailable to check Rd xrefs: 'doMC'
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs       1.2Mb
    testdata   1.3Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.2/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.2/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.2/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.2/lolog.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    help   1.2Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   4.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  lxb.c:62:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.2/lxb.Rcheck/00install.out' for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs  36.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs          3.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.4Mb
    libs   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    5.4Mb
    libs   2.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    lib    1.0Mb
    libs   1.1Mb
cdf.pval: no visible global function definition for 'median'
cdf.pval: no visible binding for global variable 'ecdf'
find_hits: no visible global function definition for 'na.omit'
mad.scores: no visible global function definition for 'as.formula'
mad.scores: no visible binding for global variable 'median'
mad.scores: no visible binding for global variable 'mad'
rm.outliers: no visible global function definition for 'as.formula'
rm.outliers: no visible binding for global variable 'median'
rm.outliers: no visible binding for global variable 'mad'
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   4.1Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/mpmi.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   4.0Mb
    libs   1.1Mb
Running 'test-all.R' [79s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > library(testthat)
  > 
  > test_check("mudata2")
  Loading required package: mudata2
  
  Attaching package: 'mudata2'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Error (test-mudata-io.R:114:3): type strs are guessed when inappropriate columns exist in columns tbl --
  Error: Error writing mudata to CSV:
   _mudata.csv: Error : Cannot open file for writing:
  * 'D:\temp\RtmpwPok89\fileee8c2e5fb91\_mudata.csv'
  
  Backtrace:
      x
   1. \-mudata2::write_mudata_dir(...) test-mudata-io.R:114:2
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 891 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'leukemiasEset'
Error(s) in re-building vignettes:
--- re-building 'Tutorial.Rmd' using rmarkdown


Quitting from lines 131-144 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
Bioconductor does not yet build and check packages for R version 4.2; see
  https://bioconductor.org/install
--- failed re-building 'Tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    5.8Mb
    libs   5.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.3Mb
    models   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   1.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    CppCode   1.6Mb
    R         5.8Mb
    include   5.7Mb
    libs      1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/nser.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   1.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.4Mb
    libs   1.2Mb
Error(s) in re-building vignettes:
--- re-building 'ojsr-vignette.Rmd' using rmarkdown
Quitting from lines 260-268 (ojsr-vignette.Rmd) 
Error: processing vignette 'ojsr-vignette.Rmd' failed with diagnostics:
object 'record' not found
--- failed re-building 'ojsr-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'unix'
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs   12.6Mb
    share  10.2Mb
Error(s) in re-building vignettes:
--- re-building 'openland_vignette.Rmd' using rmarkdown
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Quitting from lines 40-52 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
cannot open URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
--- failed re-building 'openland_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     3.9Mb
    models   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
Running 'exporting-methods.R' [4s]
  Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  == Failed tests ================================================================
  -- Error (test.match_on.R:591:5): standardization_scale with svyglm ------------
  Error: non-numeric argument to binary operator
  Backtrace:
      x
   1. \-optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   \-optmatch:::standardizer(des_t)
   3.     +-stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     \-survey:::update.survey.design(...)
   5.       \-base::eval(dots[[j]], object$variables, parent.frame())
   6.         \-base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   1.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs   3.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/pbdRPC.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   6.7Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs    6.5Mb
    share  12.8Mb
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11519 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11519 (sockconn)
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    help   1.1Mb
    libs   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
    libs      1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    shinyApp   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   1.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   1.2Mb
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.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   1.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    etc    1.9Mb
    po     1.2Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.2/Rblpapi.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
    po    2.3Mb
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  8.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       1.9Mb
    libs      1.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    include        1.7Mb
    jsonexamples   3.8Mb
    libs           1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/rcrypt.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Package which this enhances but not available for checking: 'Rcplex'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is 61.2Mb
  sub-directories of 1Mb or more:
    doc        3.4Mb
    gdal       2.2Mb
    libs      43.1Mb
    pictures   1.3Mb
    proj       8.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      3.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.1Mb
Running examples in 'rgho-Ex.R' failed
The error most likely occurred in:

> ### Name: get_gho_dimensions
> ### Title: Returns GHO Dimensions/Codes
> ### Aliases: get_gho_dimensions get_gho_codes man-gho print.gho
> 
> ### ** Examples
> 
> 
> get_gho_dimensions()
Error during request:
Server error: (503) Service Unavailable
Execution halted
Error(s) in re-building vignettes:
--- re-building 'a-intro.Rmd' using rmarkdown
Quitting from lines 30-31 (a-intro.Rmd) 
Error: processing vignette 'a-intro.Rmd' failed with diagnostics:

--- failed re-building 'a-intro.Rmd'

--- re-building 'b-dimensions.Rmd' using rmarkdown
Quitting from lines 21-22 (b-dimensions.Rmd) 
Error: processing vignette 'b-dimensions.Rmd' failed with diagnostics:

--- failed re-building 'b-dimensions.Rmd'

--- re-building 'c-codes-gho.Rmd' using rmarkdown
Quitting from lines 21-22 (c-codes-gho.Rmd) 
Error: processing vignette 'c-codes-gho.Rmd' failed with diagnostics:

--- failed re-building 'c-codes-gho.Rmd'

--- re-building 'd-codes-country.Rmd' using rmarkdown
Quitting from lines 21-28 (d-codes-country.Rmd) 
Error: processing vignette 'd-codes-country.Rmd' failed with diagnostics:

--- failed re-building 'd-codes-country.Rmd'

--- re-building 'e-details.Rmd' using rmarkdown
--- finished re-building 'e-details.Rmd'

SUMMARY: processing the following files failed:
  'a-intro.Rmd' 'b-dimensions.Rmd' 'c-codes-gho.Rmd'
  'd-codes-country.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc     1.7Mb
    fonts   1.5Mb
    libs    1.3Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   2.4Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
Found the following significant warnings:
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
See 'd:/Rcompile/CRANpkg/local/4.2/Rhpc.Rcheck/00install.out' for details.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.2/RInside.Rcheck/00install.out' for details.
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.
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 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 24.5Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    minizinc   2.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/ROracle.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'rosm.Rmd' using rmarkdown
Using default API key for pickpoint.io. If batch geocoding, please get your own (free) API key at https://app.pickpoint.io/sign-up
Quitting from lines 35-38 (rosm.Rmd) 
Error: processing vignette 'rosm.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'rosm.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/RSclient.Rcheck/00install.out' for details.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.2/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/Rserve/libs/x64/Rserve.dll':
  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', '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.
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.2/RSNNS.Rcheck/00install.out' for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.5Mb
    libs   9.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    lib    2.0Mb
    libs   4.6Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2021-05-18 r80323)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.2.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.1Mb
    projects   2.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      5.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
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'.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs      4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.1Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  13.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.1, released 2020/12/29
Path to GDAL shared files: D:/temp/RtmpaqgMLo/RLIBS_39858706613e4/rgdal/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: D:/temp/RtmpaqgMLo/RLIBS_39858706613e4/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was D:/temp/RtmpaqgMLo/RLIBS_39858706613e4/rgdal/proj
Warning in utils::download.file(url, tmp, quiet = TRUE) :
  URL 'https://www.lifewatch.be/sdmpredictors/sysdata.rda': status was 'SSL connect error'
trying URL 'http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif'
Content length 263 bytes
==================================================
Quitting from lines 79-91 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
cannot open URL 'http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif'
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
installed size is 61.6Mb
  sub-directories of 1Mb or more:
    doc      2.3Mb
    gdal     2.2Mb
    libs    44.0Mb
    proj     8.7Mb
    sqlite   1.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    www  16.5Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   8.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   1.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.7Mb
    libs   1.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.2Mb
    libs   1.4Mb
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.2/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.2/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.3Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    help   1.7Mb
    libs   1.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.1Mb
    etc   1.3Mb
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.6)
than is installed on your system (1.0.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.6)
than is installed on your system (1.0.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.6)
than is installed on your system (1.0.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      1.1Mb
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
Error(s) in re-building vignettes:
--- re-building 'custom_function_example.Rmd' using rmarkdown
Loading required package: sp

Attaching package: 'future'

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

    values

Warning in x@data@values[i] <- value :
  number of items to replace is not a multiple of replacement length
--- finished re-building 'custom_function_example.Rmd'

--- re-building 'kangaroo_model_example.Rmd' using rmarkdown
Loading required package: sp

Attaching package: 'future'

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

    values

Quitting from lines 335-355 (kangaroo_model_example.Rmd) 
Error: processing vignette 'kangaroo_model_example.Rmd' failed with diagnostics:
Survival values greater than one have been detected. Please check to ensure
that your transition matrix values or stochasticity (standard deviation) values
are sensible and re-run the simulation.
--- failed re-building 'kangaroo_model_example.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc  10.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    libs   1.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  11.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    libs      1.0Mb
    telemac   1.0Mb
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    gdal   2.1Mb
    libs  45.4Mb
    proj   8.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc        1.2Mb
    libs       7.0Mb
    tessdata  14.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.9Mb
    libs   1.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("tibble")
  Loading required package: tibble
  Starting 2 test processes
  == Skipped tests ===============================================================
  * All of them (1)
  * Do we want an .as_row argument? (1)
  * Installed rlang is version 0.4.11; but 0.4.11.9001 is required (1)
  * Non-UTF-8 locale (7)
  * On CRAN (32)
  * On Windows (1)
  * packageVersion("tibble") >= "2.99.99" is TRUE (93)
  
  == Failed tests ================================================================
  -- Failure (test-zzz-trunc-mat.R:15:3): interface of print() identical to trunc_mat() --
  `print_arg_names_without` (`actual`) not equal to `trunc_mat_arg_names_without` (`expected`).
  
  `actual`:   "x" "n" "max_extra_cols" "max_footer_lines"
  `expected`: "x" "n" "n_extra"                          
  
  [ FAIL 1 | WARN 0 | SKIP 136 | PASS 1314 ]
  Error: Test failures
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    examples  12.4Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Running examples in 'TNRS-Ex.R' failed
The error most likely occurred in:

> ### Name: TNRS
> ### Title: Resolve plant taxonomic names
> ### Aliases: TNRS
> 
> ### ** Examples
> 
> {
+ #Take a subset of the testfile to speed up runtime                  
+ tnrs_testfile <- tnrs_testfile[1:20,]
+  
+ results <- TNRS(taxonomic_names = tnrs_testfile)
+   
+ # Inspect the results
+ head(results, 10)
+ }
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: TNRS ... .TNRS_base -> postForm -> .postForm -> <Anonymous> -> fun
Execution halted
Error(s) in re-building vignettes:
--- re-building 'TNRS_vignette.Rmd' using rmarkdown
Quitting from lines 30-50 (TNRS_vignette.Rmd) 
Error: processing vignette 'TNRS_vignette.Rmd' failed with diagnostics:
error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
--- failed re-building 'TNRS_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    help   1.4Mb
    libs  12.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   6.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.6Mb
    shinyapp   3.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.4Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    gdal      3.8Mb
    libs     34.2Mb
    proj      5.0Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs  14.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
installed size is 56.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      2.2Mb
    libs     43.2Mb
    proj      8.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  URL 'https://rud.is/dl/embedded.json': status was 'SSL connect error'
Error in file(con, "r") : 
  cannot open the connection to 'http://rud.is/dl/embedded.json'
Calls: from_spec -> readLines -> file
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   2.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   6.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.3Mb
    htmlwidgets   3.9Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
Error(s) in re-building vignettes:
--- re-building 'intro.Rmd' using rmarkdown
--- finished re-building 'intro.Rmd'

--- re-building 'united_nations.Rmd' using rmarkdown

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

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
Can't join on `x$a2` x `y$a2` because of incompatible types.
i `x$a2` is of type <logical>>.
i `y$a2` is of type <character>>.
--- failed re-building 'united_nations.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
.__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   7.0Mb
Found the following significant warnings:
  Warning: S3 methods '$.tbl_df', '$<-.tbl_df', '[.tbl_df', '[<-.tbl_df', '[[.tbl_df', '[[<-.tbl_df', 'names<-.tbl_df', 'row.names<-.tbl_df', 'as.data.frame.tbl_df', 'as_tibble.NULL', 'as_tibble.data.frame', 'as_tibble.default', 'as_tibble.list', 'as_tibble.matrix', 'as_tibble.poly', 'as_tibble.table', 'as_tibble.ts', 'format.trunc_mat', 'print.trunc_mat', 'quote_n.character', 'quote_n.default', 'str.tbl_df', 'tbl_sum.tbl_df', 'vec_ptype_abbr.tbl_df' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/4.2/workflowr.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.2/x13binary.Rcheck/00install.out' for details.
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.1Mb
Running examples in 'xpose4-Ex.R' failed
The error most likely occurred in:

> ### Name: simprazExample
> ### Title: Function to create files for the simulated prazosin example in
> ###   Xpose
> ### Aliases: simprazExample
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> od = setwd(tempdir()) # move to a temp directory
> (cur.files <- dir()) # current files in temp directory
[1] "pdf1783060b57763" "xptab1"          
> 
> simprazExample(overwrite=TRUE) # write files
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'xptab1': Invalid argument
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: simprazExample -> writeTab -> cat -> file
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Running examples in 'zoon-Ex.R' failed
The error most likely occurred in:

> ### Name: ModuleArguments
> ### Title: ModuleArguments
> ### Aliases: ModuleArguments
> 
> ### ** Examples
> 
> ModuleArguments('Background')
Error in ModuleArguments("Background") : 
  URL for module does not exist: https://raw.githubusercontent.com/zoonproject/modules/master/R/Background.R
Execution halted
Packages required but not available: 'plotly', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mosaic'

Packages suggested but not available for checking:
  'car', 'ggplot2', 'HH', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'INLA', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > # automatic unit tests
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'colourpicker', 'emojifont'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'usethis', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dvmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'reldist'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readxl', 'readr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'GDINA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cosinor', 'cosinor2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DiagrammeR', 'ggplot2', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'accelerometry', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggmap', 'tibble', 'timetk'

Packages suggested but not available for checking:
  'ggplot2', 'mockery', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19'

Packages suggested but not available for checking:
  'testthat', 'BSgenome.Hsapiens.UCSC.hg38',
  'BSgenome.Mmusculus.UCSC.mm9', 'BSgenome.Mmusculus.UCSC.mm10'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'ActivityIndex-Ex.R' failed
The error most likely occurred in:

> ### Name: Sigma0
> ### Title: \bar{sigma}_i computing using raw accelerometry data
> ### Aliases: Sigma0
> 
> ### ** Examples
> 
> filename = system.file("extdata","sample_GT3X+.csv.gz",package="ActivityIndex")
> res = ReadGT3XPlus(filename)
> hertz = res$Hertz
> x = res$Raw[ 1:1000, c("Time", "X", "Y", "Z")]
> res = Sigma0(x, hertz = hertz)
> testthat::expect_equal(res, c(SD = 0.184321637135534))
Error in loadNamespace(x) : there is no package called 'testthat'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'devtools'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Anthropometry', 'univOutl'

Package suggested but not available for checking: 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'lintr'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DataVisualizations'

Packages suggested but not available for checking:
  'parallelDist', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
Error(s) in re-building vignettes:
--- re-building 'adapt_demo.Rmd' using rmarkdown
Failed with error:  'there is no package called 'dplyr''
Quitting from lines 60-70 (adapt_demo.Rmd) 
Error: processing vignette 'adapt_demo.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'adapt_demo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'WGCNA'

Package suggested but not available for checking: 'DeconRNASeq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gsDesign'
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shinyFiles', 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Benchmarking'
  All declared Imports should be used.
Packages required but not available: 'parsnip', 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'recipes', 'roxygen2', 'testthat', 'workflows'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'adephylo', 'spdep'
Namespace in Imports field not imported from: 'sp'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'spdep', 'adephylo'
Packages required but not available: 'ggplot2', 'spdep', 'dplyr'

Packages suggested but not available for checking:
  'pegas', 'hierfstat', 'testthat', 'poppr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spdep'
Package unavailable to check Rd xrefs: 'spdep'
Running 'add.R'
  Running 'adegraphics.R'
  Running 'nbgraph.R'
Running the tests in 'tests/nbgraph.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > library(spdep)
  Error in library(spdep) : there is no package called 'spdep'
  Execution halted
Namespace in Imports field not imported from: 'filehash'
  All declared Imports should be used.
Packages required but not available: 'phylobase', 'adegenet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'tidyr', 'haven'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dvmisc'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adephylo', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'AdhereRViz'
Packages required but not available:
  'colourpicker', 'readODS', 'readxl', 'haven', 'RMariaDB'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pegas'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adephylo', 'phylobase', 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'HiTC'
Packages required but not available: 'dplyr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'sf'
Running examples in 'adklakedata-Ex.R' failed
The error most likely occurred in:

> ### Name: adk_lake_shapes
> ### Title: Return path to Lake Polygons Shapefile
> ### Aliases: adk_lake_shapes
> 
> ### ** Examples
> 
> library(sf)
Error in library(sf) : there is no package called 'sf'
Execution halted
Packages suggested but not available for checking: 'flexsurv', 'testthat'
Packages required but not available: 'dplyr', 'readr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'ggplot2'

Packages suggested but not available for checking: 'shinystan', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrrlyr', 'tidyr', 'ggplot2', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'adoptr.Rmd' using rmarkdown
--- finished re-building 'adoptr.Rmd'

--- re-building 'adoptr_jss.Rmd' using rmarkdown
Quitting from lines 52-67 (adoptr_jss.Rmd) 
Error: processing vignette 'adoptr_jss.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'adoptr_jss.Rmd'

--- re-building 'composite-scores.Rmd' using rmarkdown
--- finished re-building 'composite-scores.Rmd'

--- re-building 'conditional-scores.Rmd' using rmarkdown
--- finished re-building 'conditional-scores.Rmd'

--- re-building 'defining-new-scores.Rmd' using rmarkdown
--- finished re-building 'defining-new-scores.Rmd'

--- re-building 'working-with-priors.Rmd' using rmarkdown
--- finished re-building 'working-with-priors.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'fields'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'car', 'forcats', 'GGally', 'ggplot2', 'Hmisc', 'readr',
  'sjstats', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'qvalue'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggvis', 'plotly', 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

Packages suggested but not available for checking:
  'dynlm', 'forecast', 'mlogit', 'sampleSelection', 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'ggmcmc', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pbkrtest', 'lmerTest', 'car'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'ggplot2', 'ggbeeswarm', 'cowplot',
  'jtools', 'ggpubr', 'ggpol', 'brms', 'rstanarm', 'see', 'ez',
  'ggResidpanel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'photobiology', 'useful'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
Package required but not available: 'spdep'

Package suggested but not available for checking: 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'GGIR', 'PAutilities'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'cccrm'
Packages required but not available: 'ggplot2', 'agricolae'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'klaR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'AER', 'agricolae', 'broom', 'car', 'desplot', 'dplyr',
  'equivalence', 'ggplot2', 'HH', 'nullabor', 'pbkrtest', 'qicharts',
  'SpATS', 'testthat'
Running examples in 'agridat-Ex.R' failed
The error most likely occurred in:

> ### Name: cochran.latin
> ### Title: Latin square design in wheat
> ### Aliases: cochran.latin
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(agridat)
> 
> data(cochran.latin)
> dat <- cochran.latin
> 
> libs(desplot)
Installing package into 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/agridat/agridat.Rcheck'
(as 'lib' is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: libs -> install.packages -> contrib.url
Execution halted
Packages required but not available: 'lmerTest', 'pbkrtest', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggpubr', 'cowplot', 'ggforce'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'drc', 'ggplot2', 'car', 'dplyr', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ScottKnott', 'Hmisc', 'ARTool', 'ggrepel', 'cowplot',
  'drc'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', 'dplyr', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'AhoCorasickTrieTests.R'
  Running 'benchmark.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyr', 'dplyr', 'randomNames'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'lmerTest'
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'onewaytests'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rvest', 'tidyr', 'readr', 'readxl'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggseas', 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggmcmc', 'hydroPSO', 'imputeTS', 'GGally', 'ggplot2',
  'testthat'
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'GGally', 'ggmap', 'ggplot2', 'leaflet',
  'MazamaCoreUtils', 'MazamaLocationUtils', 'MazamaSpatialUtils',
  'openair', 'PWFSLSmoke', 'readr', 'tibble', 'tidyr', 'worldmet'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'EstCRM'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggraph', 'tidygraph', 'ggforce', 'textstem',
  'tibble', 'tidytext', 'widyr', 'ggwordcloud'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'Hmisc', 'ggplot2'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'airr', 'dplyr', 'GenomicAlignments', 'readr', 'tibble',
  'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking: 'eemR', 'EEM'
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'aldvmm_vignette.Rmd' using rmarkdown
Quitting from lines 20-60 (aldvmm_vignette.Rmd) 
Error: processing vignette 'aldvmm_vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'aldvmm_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'caret'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'httptest', 'roxygen2', 'testthat'
Running 'capture_util.R'
  Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rvest', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BiodiversityR', 'adegenet'

Packages suggested but not available for checking:
  'poppr', 'dplyr', 'ggplot2', 'GGally', 'ggforce', 'ggrepel', 'ggsci',
  'gggibbous', 'gganimate', 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'tibble', 'ggplot2', 'tidyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'dplyr'
Running 'testall.R'
Running the tests in 'tests/testall.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'alluvial.Rmd' using rmarkdown
Quitting from lines 17-25 (alluvial.Rmd) 
Error: processing vignette 'alluvial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'alluvial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'cli', 'dlookr', 'dplyr', 'ggmosaic', 'tibble', 'tidyr',
  'unbalanced'

Package suggested but not available for checking: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'car'
Package suggested but not available for checking: 'alphahull'
Packages suggested but not available for checking:
  'testthat', 'mockery', 'httptest'
Packages required but not available:
  'dplyr', 'readr', 'tibble', 'tidyr', 'timetk'

Packages suggested but not available for checking: 'tidyquant', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Package required but not available: 'repr'

Packages suggested but not available for checking:
  'readr', 'tibble', 'testthat', 'tidyr', 'dplyr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'readr', 'readxl', 'ggplot2', 'ggrepel', 'tidyr',
  'kableExtra', 'tidyverse'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sjmisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'log', 'cli'

Package suggested but not available for checking: 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Zelig'
Package suggested but not available for checking: 'network'
Packages required but not available: 'agricolae', 'ggcorrplot', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'MplusAutomation', 'devtools', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'cleaner', 'dplyr', 'ggplot2', 'ggtext', 'pillar', 'readxl', 'rvest',
  'skimr', 'tidyr'
Packages unavailable to check Rd xrefs: 'dplyr', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'AMR.Rmd' using rmarkdown
Quitting from lines 66-73 (AMR.Rmd) 
Error: processing vignette 'AMR.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'AMR.Rmd'

--- re-building 'MDR.Rmd' using rmarkdown
Quitting from lines 95-97 (MDR.Rmd) 
Error: processing vignette 'MDR.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'MDR.Rmd'

--- re-building 'datasets.Rmd' using rmarkdown
Quitting from lines 17-91 (datasets.Rmd) 
Error: processing vignette 'datasets.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'datasets.Rmd'

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

SUMMARY: processing the following files failed:
  'AMR.Rmd' 'MDR.Rmd' 'datasets.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'sf', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'ggplot2', 'ggraph', 'leaflet', 'moveHMM', 'sessioninfo',
  'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Hmisc', 'testthat'
Packages required but not available: 'car', 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ## Test `analogue` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'plotly', 'car'

Package which this enhances but not available for checking: 'SparkR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dbplyr', 'cli', 'pillar'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'ggplot2', 'cowplot'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spbabel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'brms', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forcats', 'tibble', 'leaflet', 'leaflet.extras', 'dplyr', 'ggplot2',
  'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'gistr', 'testthat', 'devtools', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggmap', 'crawl', 'dplyr', 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'testthat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

Package suggested but not available for checking: 'GEOquery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EnvStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'timetk', 'sweep', 'tibbletime', 'tibble', 'tidyr',
  'ggplot2', 'cli'

Packages suggested but not available for checking:
  'tidyverse', 'tidyquant', 'testthat', 'devtools', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'car', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'HH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #Copyright © 2016 RTE Réseau de transport d’électricité
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rhdf5', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #Copyright © 2016 RTE Réseau de transport d’électricité
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(antaresRead)
  Loading required package: antaresRead
  > require(plyr)
  Loading required package: plyr
  > 
  > 
  > #Maybe include this in some test-file.R 
  > #is.solaris<-function(){
  > #  grepl('SunOS',Sys.info()['sysname'])
  > #}
  > 
  > #if(!is.solaris()){
  > 
  > test_check("antaresRead")
  Error in test_check("antaresRead") : could not find function "test_check"
  Execution halted
Packages required but not available:
  'plotly', 'leaflet', 'geojsonio', 'leaflet.minicharts'

Packages suggested but not available for checking:
  'testthat', 'rhdf5', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'smacof'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'biclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > if (!requireNamespace("testthat", quietly = TRUE)) {
  +   stop("The `testthat` package is not available, therefore `anticlust` cannot be tested.")
  + }
  Error: The `testthat` package is not available, therefore `anticlust` cannot be tested.
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'competitiontoolbox'
Packages unavailable to check Rd xrefs: 'ggplot2', 'competitiontoolbox'
Packages required but not available: 'GGally', 'bayesplot'

Packages suggested but not available for checking:
  'dendextend', 'ggdendro', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'readr', 'vroom', 'usethis', 'roxygen2'

Packages suggested but not available for checking:
  'testthat', 'nycflights13'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'geepack'
Package required but not available: 'roxygen2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'mapview', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cellranger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'dplyr', 'tibble', 'broom',
  'car', 'highcharter', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'MBESS', 'tibble'

Packages suggested but not available for checking: 'afex', 'ez', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'broom', 'dplyr', 'tibble', 'MBESS'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'apaTables'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  WARNING: failed to apply patch patches/CRAN/apcf.diff
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/apcf/apcf.Rcheck/00install.out' for details.
Packages required but not available:
  'haven', 'tidyverse', 'dplyr', 'ggplot2', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'AER', 'ggplot2', 'ChainLadder'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'pls'
  All declared Imports should be used.
Package required but not available: 'adegenet'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'episensr', 'golem', 'ggraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'patchwork'

Package suggested but not available for checking: 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'performanceEstimation', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'hardhat', 'tibble', 'proxyC', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'recipes', 'testthat', 'AmesHousing'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'caret'
Running examples in 'AppliedPredictiveModeling-Ex.R' failed
The error most likely occurred in:

> ### Name: concrete
> ### Title: Compressive Strength of Concrete from Yeh (1998)
> ### Aliases: concrete mixtures
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(concrete)
> 
> library(caret)
Error in library(caret) : there is no package called 'caret'
Execution halted
Packages required but not available: 'logistf', 'rms', 'shrink'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'daymetr', 'FedData', 'ggplot2', 'nasapower', 'sf'
Packages unavailable to check Rd xrefs: 'daymetr', 'FedData', 'nasapower'
Running 'test_AK_point_sim.R'
  Running 'test_apsim_swim.R'
  Running 'test_apsimx_factorial.R'
  Running 'test_classic_examples.r'
  Running 'test_compare_apsim.R'
  Running 'test_edit.R'
  Running 'test_edit_apsim_replace_soil_profile.R'
  Running 'test_edit_apsim_xml.R'
  Running 'test_edit_apsimx_json.R'
  Running 'test_edit_apsimx_replacement.R'
  Running 'test_edit_batch.R'
  Running 'test_examples.R'
  Running 'test_extract_values_apsimx.R'
  Running 'test_get_daymet_apsim_met.R'
  Running 'test_get_gsod_apsim_met.R'
  Running 'test_get_isric_soil_profile.R'
  Running 'test_grep_json_list.R'
  Running 'test_inspect.R'
  Running 'test_inspect_apsim_factorial.R'
  Running 'test_inspect_apsim_xml.R'
  Running 'test_inspect_apsimx_json.R'
  Running 'test_optim_apsimx.R'
Running the tests in 'tests/test_optim_apsimx.R' failed.
Complete output:
  > ## Testing the capability of optimizing parameters
  > require(apsimx)
  Loading required package: apsimx
  APSIM(X) not found. 
   
               If APSIM(X) is installed in an alternative location, 
  
              set paths manually using 'apsimx_options' or 'apsim_options' 
  
              You can still try as the package will look into the registry (under Windows)
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'apsimx-scripts.Rmd' using rmarkdown
--- finished re-building 'apsimx-scripts.Rmd'

--- re-building 'apsimx.Rmd' using rmarkdown
Quitting from lines 15-18 (apsimx.Rmd) 
Error: processing vignette 'apsimx.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'apsimx.Rmd'

--- re-building 'optim-apsim.Rmd' using rmarkdown
Quitting from lines 15-20 (optim-apsim.Rmd) 
Error: processing vignette 'optim-apsim.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'optim-apsim.Rmd'

SUMMARY: processing the following files failed:
  'apsimx.Rmd' 'optim-apsim.Rmd'

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'AER'
Packages required but not available: 'brranching', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'erer', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'forcats', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'srvyr', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sharpshootR', 'markovchain', 'testthat', 'Hmisc', 'tibble'
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'readr'

Packages suggested but not available for checking: 'testthat', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgbif', 'rworldmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rvest', 'dlstats', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ArchaeoPhases', 'Bchron'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'hdrcde', 'readr', 'ggthemes', 'toOrdinal', 'ggplot2', 'ggalt',
  'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'skimr', 'testthat', 'feather', 'readr'

Packages suggested but not available for checking:
  'broom', 'caret', 'gtsummary', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggplot2'
Packages required but not available: 'dplyr', 'lidR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rvest', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'ggplot2', 'devtools'
Running examples in 'archivist-Ex.R' failed
The error most likely occurred in:

> ### Name: ahistory
> ### Title: Show Artifact's History
> ### Aliases: ahistory
> 
> ### ** Examples
> 
> 
> createLocalRepo("ahistory_check", default = TRUE)
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'vroom'

Packages suggested but not available for checking:
  'ggplot2', 'forcats', 'leaflet', 'sf', 'tigris', 'testthat',
  'geofacet', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'rvest', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'arctools_intro.Rmd' using rmarkdown
Quitting from lines 39-49 (arctools_intro.Rmd) 
Error: processing vignette 'arctools_intro.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'arctools_intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'dynlm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'sf', 'tibble', 'tidyr', 'tabshiftr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'dplyr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ingredients', 'iBreakDown', 'gistr', 'auditor', 'DALEX',
  'fairmodels'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'argparse-Ex.R' failed
The error most likely occurred in:

> ### Name: ArgumentParser
> ### Title: Create a command line parser
> ### Aliases: ArgumentParser
> 
> ### ** Examples
> 
> 
> parser <- ArgumentParser(description='Process some integers')
Error in findpython::find_python_cmd(required_modules = required_modules) : 
  Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary')  or set the PYTHON, PYTHON2, or PYTHON3 environmental variables.   Python must have access to the modules: argparse, json | simplejson
Calls: ArgumentParser -> .find_python_cmd -> <Anonymous>
Execution halted
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ari', 'rvest', 'text2speech', 'docxtractr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'text2speech', 'rvest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'readr', 'dplyr', 'dbplyr', 'nycflights13', 'testthat', 'vroom',
  'MonetDBLite'
Package unavailable to check Rd xrefs: 'readr'
Error(s) in re-building vignettes:
--- re-building 'arkdb.Rmd' using rmarkdown
Quitting from lines 45-52 (arkdb.Rmd) 
Error: processing vignette 'arkdb.Rmd' failed with diagnostics:
there is no package called 'dbplyr'
--- failed re-building 'arkdb.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'qvalue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'leaflet'
Running examples in 'ar.matrix-Ex.R' failed
The error most likely occurred in:

> ### Name: Q.AR1
> ### Title: Precision matrix for an AR1 process
> ### Aliases: Q.AR1 r.AR1
> 
> ### ** Examples
> 
> require("ggplot2")
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
> # simulate AR1 GMRF
> obs <- r.AR1(100, M=30, sigma=1, rho=.98)
> # resulting matrix is n x M
> dim(obs)
[1] 100  30
> # subtract off the first time point to more easily observe correlation
> obs_adj <- obs - obs[,1]
> # move objects to a data frame
> ar1_df <- data.frame(obs=c(t(obs_adj)), realization=rep(1:100, each=30),
+                      time=rep(1:30, 100))
> # plot each realization
> ggplot(data=ar1_df, aes(time, obs, group=realization, color=realization)) +
+     geom_line()
Error in ggplot(data = ar1_df, aes(time, obs, group = realization, color = realization)) : 
  could not find function "ggplot"
Execution halted
Packages required but not available:
  'tidyverse', 'dplyr', 'readr', 'tidyr', 'eurostat', 'sf', 'ggplot2',
  'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'gmm' 'graphics' 'sandwich' 'stats4' 'utils'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'viridis', 'testthat'
Running examples in 'ARPobservation-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.behavior_stream
> ### Title: Plot method for 'behavior_stream' objects
> ### Aliases: plot.behavior_stream
> 
> ### ** Examples
> 
> b_streams <- r_behavior_stream(n = 5, mu = 3, lambda = 10, 
+                                F_event = F_exp(), F_interim = F_exp(), 
+                                stream_length = 100)
> plot(b_streams)
Error: This function needs the ggplot2 package to work. Please install it.
Execution halted
Packages suggested but not available for checking:
  'decor', 'dplyr', 'pkgload', 'testthat', 'tibble'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Licensed to the Apache Software Foundation (ASF) under one
  > # or more contributor license agreements.  See the NOTICE file
  > # distributed with this work for additional information
  > # regarding copyright ownership.  The ASF licenses this file
  > # to you under the Apache License, Version 2.0 (the
  > # "License"); you may not use this file except in compliance
  > # with the License.  You may obtain a copy of the License at
  > #
  > #   http://www.apache.org/licenses/LICENSE-2.0
  > #
  > # Unless required by applicable law or agreed to in writing,
  > # software distributed under the License is distributed on an
  > # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
  > # KIND, either express or implied.  See the License for the
  > # specific language governing permissions and limitations
  > # under the License.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'arrow.Rmd' using rmarkdown
--- finished re-building 'arrow.Rmd'

--- re-building 'dataset.Rmd' using rmarkdown
Quitting from lines 93-95 (dataset.Rmd) 
Error: processing vignette 'dataset.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'dataset.Rmd'

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'broom', 'testthat', 'geepack'
Running examples in 'arsenal-Ex.R' failed
The error most likely occurred in:

> ### Name: modelsum
> ### Title: Fit models over each of a set of independent variables with a
> ###   response variable
> ### Aliases: modelsum
> 
> ### ** Examples
> 
> 
> data(mockstudy)
> 
> tab1 <- modelsum(bmi ~ sex + age, data = mockstudy)
Error in check_pkg("broom") : 
  Package 'broom' is required for this functionality, but is not installed.
Calls: modelsum -> modelsum_guts -> check_pkg
Execution halted
Error(s) in re-building vignettes:
--- re-building 'comparedf.Rmd' using rmarkdown
--- finished re-building 'comparedf.Rmd'

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

--- re-building 'labels.Rmd' using rmarkdown

Attaching package: 'magrittr'

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

    set_attr

Quitting from lines 43-49 (labels.Rmd) 
Error: processing vignette 'labels.Rmd' failed with diagnostics:
Package 'broom' is required for this functionality, but is not installed.
--- failed re-building 'labels.Rmd'

--- re-building 'modelsum.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: broom
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'broom'
Loading required package: MASS
Loading required package: pROC
Type 'citation("pROC")' for a citation.

Attaching package: 'pROC'

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

    cov, smooth, var

Loading required package: rpart
Quitting from lines 64-65 (modelsum.Rmd) 
Error: processing vignette 'modelsum.Rmd' failed with diagnostics:
Package 'broom' is required for this functionality, but is not installed.
--- failed re-building 'modelsum.Rmd'

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

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

--- re-building 'write2.Rmd' using rmarkdown
--- finished re-building 'write2.Rmd'

SUMMARY: processing the following files failed:
  'labels.Rmd' 'modelsum.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'rstan', 'rstantools', 'RcppParallel', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr', 'lmerTest', 'phia'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'arulesViz', 'testthat'
Packages required but not available:
  'ggplot2', 'ggnetwork', 'tibble', 'tidyr', 'dplyr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'
Package required but not available: 'tibble'

Package suggested but not available for checking: 'cli'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package suggested but not available for checking: 'Hmisc'
Packages required but not available: 'haven', 'readr', 'vroom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'spdep'
Error(s) in re-building vignettes:
--- re-building 'adaptive_shrinkage.Rmd' using rmarkdown
Quitting from lines 28-30 (adaptive_shrinkage.Rmd) 
Error: processing vignette 'adaptive_shrinkage.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'adaptive_shrinkage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'exact2x2', 'exactci', 'bpcp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'llama', 'mlr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sna'
Running examples in 'asnipe-Ex.R' failed
The error most likely occurred in:

> ### Name: network_permutation
> ### Title: Perform Permutation
> ### Aliases: network_permutation
> 
> ### ** Examples
> 
> 
> ### USING TIMES, ETC.
> 
> data("group_by_individual")
> data("times")
> 
> # subset GBI (to reduce run time of the example)
> gbi <- gbi[,1:80]
> 
> ## define to 2 x N x N network to hold two association matrices
> networks <- array(0, c(2, ncol(gbi), ncol(gbi)))
> 
> ## calculate network for first half of the time
> networks[1,,] <- get_network(gbi, data_format="GBI", 
+ 	association_index="SRI", times=times, start_time=0, 
+ 	end_time=max(times)/2)
Generating  80  x  80  matrix
> networks[2,,] <- get_network(gbi, data_format="GBI",
+ 	association_index="SRI", times=times, 
+ 	start_time=max(times)/2, end_time=max(times))
Generating  80  x  80  matrix
> 
> ## calculate the weighted degree
> library(sna)
Error in library(sna) : there is no package called 'sna'
Execution halted
Package suggested but not available for checking: 'sem'
Packages required but not available: 'dae', 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'lmerTest', 'pbkrtest'

Package which this enhances but not available for checking: 'asreml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'devtools'
Packages required but not available: 'caret', 'ggplot2'

Packages suggested but not available for checking: 'klaR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arulesViz', 'plotly', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'asteRiskData', 'plotly', 'dplyr', 'ggmap'
Error(s) in re-building vignettes:
--- re-building 'asteRisk.Rmd' using rmarkdown
To use all functionalities available in this package, including the
high-precision numerical orbit propagator, you must install the
asteRiskData package. To install it, run
`install.packages('asteRiskData',
repos='https://rafael-ayala.github.io/drat/')`.
Quitting from lines 297-337 (asteRisk.Rmd) 
Error: processing vignette 'asteRisk.Rmd' failed with diagnostics:
there is no package called 'ggmap'
--- failed re-building 'asteRisk.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'haplo.stats', 'fields'
Running examples in 'asymLD-Ex.R' failed
The error most likely occurred in:

> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'haplo.stats'
> data(hla.demo)
Warning in data(hla.demo) : data set 'hla.demo' not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Package required but not available: 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'example.Rmd' using rmarkdown
Quitting from lines 48-58 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'example.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'doBy', 'Hmisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'stR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sensitivity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arm', 'tibble', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'ggbeeswarm', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  wmm.c:428:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int)'} [-Wincompatible-pointer-types]
  wmm.c:429:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int,  int)'} [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/audio/audio.Rcheck/00install.out' for details.
Packages required but not available: 'DALEX', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'readr', 'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'agricolae'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using knitr
Quitting from lines 72-79 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'my-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'readr', 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'forecast', 'caret'

Package which this enhances but not available for checking: 'rPython'
Packages unavailable to check Rd xrefs: 'forecast', 'caret'
Running examples in 'aurelius-Ex.R' failed
The error most likely occurred in:

> ### Name: extract_params.Arima
> ### Title: extract_params.Arima
> ### Aliases: extract_params.Arima
> 
> ### ** Examples
> 
> model <- stats::arima(presidents, c(3, 0, 0))
> extracted_model <- extract_params(model)
> 
> model <- forecast::Arima(USAccDeaths, order=c(2,2,2), seasonal=c(0,2,2))
Error in loadNamespace(x) : there is no package called 'forecast'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > suppressMessages(suppressWarnings(library(testthat)))
  Error in library(testthat) : there is no package called 'testthat'
  Calls: suppressMessages -> withCallingHandlers
  Execution halted
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'logistf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'RcppParallel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'broom', 'ggplot2', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'LatticeKrig', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'lintr'

Packages suggested but not available for checking:
  'readxl', 'rvest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'Hmisc', 'tibble', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'gear', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'EBMAforecast', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'igraph'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 248-266 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'fgsea', 'clusterProfiler', 'msigdbr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly', 'ggfortify'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tableone', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'roxygen2'
Packages required but not available: 'forecast', 'ggplot2', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ijtiff'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'styler', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'prophet', 'dplyr', 'tidyr', 'forecast', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'tidytext', 'tibble'

Packages suggested but not available for checking:
  'usethis', 'BiocInstaller', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'simts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'ggplot2', 'tidyr', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'full-example.Rmd' using rmarkdown
Quitting from lines 222-243 (full-example.Rmd) 
Error: processing vignette 'full-example.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building 'full-example.Rmd'

SUMMARY: processing the following file failed:
  'full-example.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'janitor', 'tidyr', 'ggrepel'
Error(s) in re-building vignettes:
--- re-building 'a_intro.Rmd' using rmarkdown
Quitting from lines 121-124 (a_intro.Rmd) 
Error: processing vignette 'a_intro.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'a_intro.Rmd'

--- re-building 'b_analyze-hass-cntry.Rmd' using rmarkdown
Quitting from lines 22-29 (b_analyze-hass-cntry.Rmd) 
Error: processing vignette 'b_analyze-hass-cntry.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'b_analyze-hass-cntry.Rmd'

--- re-building 'b_analyze-hass-region.Rmd' using rmarkdown
Quitting from lines 24-31 (b_analyze-hass-region.Rmd) 
Error: processing vignette 'b_analyze-hass-region.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'b_analyze-hass-region.Rmd'

--- re-building 'b_analyze-hass.Rmd' using rmarkdown
Quitting from lines 24-31 (b_analyze-hass.Rmd) 
Error: processing vignette 'b_analyze-hass.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'b_analyze-hass.Rmd'

SUMMARY: processing the following files failed:
  'a_intro.Rmd' 'b_analyze-hass-cntry.Rmd' 'b_analyze-hass-region.Rmd'
  'b_analyze-hass.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'gapminder'
Packages required but not available:
  'ggplot2', 'viridis', 'fields', 'haven', 'readxl', 'readODS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'openssl'
  All declared Imports should be used.
Packages suggested but not available for checking: 'dplyr', 'testthat'
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.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'httr' 'openssl'
  All declared Imports should be used.
Packages suggested but not available for checking: 'readr', 'testthat'
Packages required but not available: 'dplyr', 'dynutils'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

Package suggested but not available for checking: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SPOT', 'dplyr', 'ggplot2', 'golem', 'markovchain', 'padr', 'rvest',
  'testthat'

Packages suggested but not available for checking:
  'simmer.plot', 'tidyverse', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'network'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'fields', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'bacon.Rmd' using rmarkdown
Quitting from lines 54-60 (bacon.Rmd) 
Error: processing vignette 'bacon.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'bacon.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dlstats', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'tkrplot'
  All declared Imports should be used.
Packages required but not available:
  'rstan', 'rstantools', 'bayesplot', 'ggplot2', 'testthat',
  'StanHeaders', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'parsnip', 'butcher', 'dials', 'dplyr', 'hardhat', 'rsample',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'AmesHousing', 'recipes', 'testthat', 'yardstick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > rm(list=ls())
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'testthat', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stats4'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'ggExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'fields', 'spdep'
Packages unavailable to check Rd xrefs: 'fields', 'spdep'
Running examples in 'bamlss-Ex.R' failed
The error most likely occurred in:

> ### Name: neighbormatrix
> ### Title: Compute a Neighborhood Matrix from Spatial Polygons
> ### Aliases: neighbormatrix plotneighbors
> ### Keywords: models regression aplot
> 
> ### ** Examples
> 
> data("LondonFire")
> 
> ## Compute polygon boundary based
> ## neighborhood matrix.
> nm <- neighbormatrix(LondonBoroughs)
Error in loadNamespace(x) : there is no package called 'spdep'
Calls: neighbormatrix ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'bayesplot'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dplyr'
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rfPermute', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sva'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'shinytest', 'testthat'
Packages required but not available: 'dplyr', 'sf', 'janitor', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mvnfast'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'viridis', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'baRulho_quantifying_sound_degradation.Rmd' using rmarkdown
Loading required package: warbleR
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds

NOTE: functions have been renamed (run 'print(new_function_names)' to see new names). Both old and new names are available in this version 
 Please see citation('warbleR') for use in publication
Quitting from lines 83-94 (baRulho_quantifying_sound_degradation.Rmd) 
Error: processing vignette 'baRulho_quantifying_sound_degradation.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'baRulho_quantifying_sound_degradation.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rvest', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'Lahman'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'mice', 'Hmisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'googleAuthR', 'cli', 'readr', 'bigrquery'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'stars'

Packages suggested but not available for checking:
  'ggplot2', 'mapview', 'mapedit', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rms', 'do'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'forcats', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'tibble'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rmcfs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'ggrepel', 'ggplotify', 'network',
  'sna', 'dendextend', 'GGally', 'ggnetwork', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'GGally', 'roxygen2', 'dplyr', 'pkgdown', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'BAS-vignette.Rmd' using rmarkdown
Quitting from lines 266-272 (BAS-vignette.Rmd) 
Error: processing vignette 'BAS-vignette.Rmd' failed with diagnostics:
there is no package called 'GGally'
--- failed re-building 'BAS-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rvest', 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
Package unavailable to check Rd xrefs: 'tibble'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Anthropometry', 'dplyr', 'ggplot2', 'ggthemes', 'rvest',
  'rworldmap', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'egg', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'rstan', 'rstantools', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'rstan', 'rstantools', 'tidyr', 'dplyr', 'ggplot2', 'RcppParallel',
  'StanHeaders'

Packages suggested but not available for checking:
  'highcharter', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bayesDP', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'RcppParallel', 'rstan', 'rstantools',
  'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'MatrixModels'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'doMC', 'testthat', 'arm'
Error(s) in re-building vignettes:
--- re-building 'compare_lme4.Rmd' using knitr
Loading required package: coda
Loading required package: Matrix
************
Welcome to BayesFactor 0.9.12-4.2. If you have questions, please contact Richard Morey (richarddmorey@gmail.com).

Type BFManual() to open the manual.
************
Quitting from lines 34-37 (compare_lme4.Rmd) 
Error: processing vignette 'compare_lme4.Rmd' failed with diagnostics:
there is no package called 'arm'
--- failed re-building 'compare_lme4.Rmd'

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

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

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

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

SUMMARY: processing the following file failed:
  'compare_lme4.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'bayesplot', 'ggplot2', 'forecast', 'rstan', 'rstantools',
  'RcppParallel', 'StanHeaders', 'prophet'

Package suggested but not available for checking: 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayesplot', 'ggplot2', 'RcppParallel', 'rstan', 'rstantools',
  'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TrackReconstruction'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'readxl', 'ggplot2', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'heatmaply', 'plotly', 'shinytest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'brms', 'parsnip', 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'recipes', 'roxygen2', 'rstan', 'testthat', 'workflows'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'tibble', 'ggforce'

Packages suggested but not available for checking: 'testthat', 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sensitivity', 'roxygen2', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(BayesianTools)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: 'rstan'
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'PLMIX', 'cowplot'

Packages suggested but not available for checking: 'testthat', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'FastGP'
  All declared Imports should be used.
Packages required but not available:
  'parsnip', 'bayesforecast', 'brms', 'Rlgt', 'rstan', 'dplyr',
  'tibble', 'dials', 'workflows', 'modeltime', 'timetk', 'cli'

Packages suggested but not available for checking:
  'tidymodels', 'tidyverse', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'leaflet', 'sf'

Packages suggested but not available for checking: 'testthat', 'ggforce'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Packages suggested but not available for checking: 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'brms', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'rstan', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'doBy'

Packages suggested but not available for checking: 'cyjShiny', 'qtlnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'StatMatch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gginnards'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggridges', 'tibble'

Packages suggested but not available for checking:
  'ggfortify', 'rstan', 'rstanarm', 'rstantools', 'shinystan',
  'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bayesLife', 'rworldmap', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggridges', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'rstan', 'rstanarm', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RcppNumerical'
  All declared Imports should be used.
Packages required but not available:
  'ggplot2', 'janitor', 'dplyr', 'rstanarm', 'groupdata2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'TeachingSampling'
Namespaces in Imports field not imported from:
  'MASS' 'Matrix' 'matrixcalc' 'stats'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'TeachingSampling'
Packages required but not available: 'dplyr', 'ggplot2', 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: 'spduration'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'blavaan', 'brms', 'dplyr', 'GGally', 'ggplot2', 'ggridges',
  'mediation', 'rstan', 'rstanarm', 'see', 'testthat', 'tidyr'
Packages suggested but not available for checking: 'rworldmap', 'ggplot2'
Package unavailable to check Rd xrefs: 'rworldmap'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'StanHeaders', 'ggplot2', 'bayesplot', 'viridis', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'BayesX-Ex.R' failed
The error most likely occurred in:

> ### Name: Interface between nb and gra format
> ### Title: Convert nb and gra format into each other
> ### Aliases: nb2gra gra2nb
> ### Keywords: spatial
> 
> ### ** Examples
> 
> ## first nb to gra:
> library(spdep)
Error in library(spdep) : there is no package called 'spdep'
Execution halted
Packages required but not available: 'rstan', 'ggplot2', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Luminescence', 'ArchaeoPhases'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfortify', 'tibble', 'tidyr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dataRetrieval'

Packages suggested but not available for checking:
  'devtools', 'dplyr', 'imputeTS', 'readxl', 'sessioninfo', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rms', 'ggplot2', 'Hmisc', 'testthat'
Running 'BIC.R'
  Comparing 'BIC.Rout' to 'BIC.Rout.save' ... OK
  Running 'ICtab.R'
  Comparing 'ICtab.Rout' to 'ICtab.Rout.save' ... OK
  Running 'RUnit-tests.R'
  Running 'binomtest1.R'
  Comparing 'binomtest1.Rout' to 'binomtest1.Rout.save' ... OK
  Running 'boundstest.R'
  Running 'controleval.R'
  Comparing 'controleval.Rout' to 'controleval.Rout.save' ... OK
  Running 'eval.R'
  Comparing 'eval.Rout' to 'eval.Rout.save' ... OK
  Running 'formulatest.R'
  Comparing 'formulatest.Rout' to 'formulatest.Rout.save' ... OK
  Running 'glmcomp.R'
Running the tests in 'tests/glmcomp.R' failed.
Complete output:
  > library(bbmle)
  Loading required package: stats4
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'secr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggrepel', 'geofacet', 'ggplot2', 'dplyr', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'greybox'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RcmdrMisc', 'Rcmdr', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dbplyr', 'dplyr', 'tibble', 'leaflet', 'leaflet.extras',
  'readr', 'readxl', 'sf'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'biclust'
Running examples in 'BcDiag-Ex.R' failed
The error most likely occurred in:

> ### Name: anomedOnlybic
> ### Title: The anomedOnlybic function
> ### Aliases: anomedOnlybic
> ### Keywords: anomedOnlybic
> 
> ### ** Examples
> 
> data(breastc)
> library(biclust)
Error in library(biclust) : there is no package called 'biclust'
Execution halted
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'INLA', 'ldr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'coda' 'knitr' 'plyr'
  All declared Imports should be used.
Packages required but not available:
  'ggplot2', 'ggridges', 'ggforce', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'bcdata'

Packages suggested but not available for checking:
  'ggplot2', 'lwgeom', 'testthat', 'stars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'BRugs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'batchelor', 'kBET', 'splatter', 'scater', 'lisi', 'harmony',
  'dlfUtils'
Packages required but not available: 'bdDwC', 'finch', 'rgbif', 'spocc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'leaflet', 'rgbif', 'spocc', 'finch', 'bdDwC', 'bdchecks'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'shinyFiles'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'ggplot2', 'ggpubr', 'sf', 'tmaptools',
  'tmap'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rtweet', 'testthat', 'tuber'
Running 'test_all.R'
Running the tests in 'tests/test_all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'taxize', 'treemap', 'ggplot2'

Package suggested but not available for checking: 'rinat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DWreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'haven', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'beadarray'

Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'drc', 'ggplot2', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.r'
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'lintr', 'readr', 'testthat'
Running examples in 'beautier-Ex.R' failed
The error most likely occurred in:

> ### Name: beautier
> ### Title: 'beautier': A package to create a 'BEAST2' input file.
> ### Aliases: beautier
> 
> ### ** Examples
> 
> # Get an example FASTA file
> input_filename <- get_fasta_filename()
> 
> # The file created by beautier, a BEAST2 input file
> output_filename <- get_beautier_tempfilename()
> 
> # Use the default BEAUti settings to create a BEAST2 input file
> create_beast2_input_file_from_model(
+   input_filename,
+   output_filename,
+   inference_model = create_inference_model()
+ )
Error in loadNamespace(x) : there is no package called 'testthat'
Calls: create_beast2_input_file_from_model ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'demo.Rmd' using rmarkdown
Quitting from lines 67-71 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'demo.Rmd'

--- re-building 'examples.Rmd' using rmarkdown
Quitting from lines 62-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'examples.Rmd'

--- re-building 'inference_models.Rmd' using rmarkdown
Quitting from lines 220-229 (inference_models.Rmd) 
Error: processing vignette 'inference_models.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'inference_models.Rmd'

SUMMARY: processing the following files failed:
  'demo.Rmd' 'examples.Rmd' 'inference_models.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'readr'

Packages suggested but not available for checking: 'biomaRt', 'GEOquery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DiagrammeR', 'ggplot2', 'googlesheets4', 'ufs', 'viridis'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'sf', 'stars', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'belg1.Rmd' using rmarkdown
Quitting from lines 13-32 (belg1.Rmd) 
Error: processing vignette 'belg1.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'belg1.Rmd'

SUMMARY: processing the following file failed:
  'belg1.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'benchmarkme', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'benchmarkmeData', 'dplyr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pillar', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggbeeswarm', 'ggplot2', 'ggridges', 'mockery',
  'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'ggplot2'
Packages required but not available:
  'benthos', 'readr', 'dplyr', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ergm', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'caret'
Namespace in Imports field not imported from: 'BiDAG'
  All declared Imports should be used.
Packages required but not available:
  'LambertW', 'dplyr', 'recipes', 'tibble', 'butcher'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'compiler'
  All declared Imports should be used.
Packages required but not available: 'tidyr', 'dplyr', 'readxl', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'coda' 'splines'
  All declared Imports should be used.
Packages suggested but not available for checking: 'DALEX', 'ggplot2'
Packages required but not available:
  'ggplot2', 'plotly', 'forecast', 'rvest', 'dplyr'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'doBy', 'Hmisc'
Packages required but not available:
  'rvest', 'tibble', 'janitor', 'dplyr', 'tidyRSS'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'
Packages unavailable to check Rd xrefs: 'ggplot2', 'dplyr'
Packages suggested but not available for checking:
  'devtools', 'testthat', 'dplyr', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'bggum.Rmd' using rmarkdown
Quitting from lines 125-142 (bggum.Rmd) 
Error: processing vignette 'bggum.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'bggum.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'RcppParallel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'prevtoinc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rBiasCorrection'

Packages suggested but not available for checking: 'lintr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'viridis', 'dendextend', 'biclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'bibliometrix'
Packages required but not available:
  'dplyr', 'factoextra', 'FactoMineR', 'forcats', 'ggplot2', 'ggrepel',
  'plotly', 'readr', 'readxl', 'rscopus', 'tidyr', 'tidytext'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'biclust', 'dplyr', 'nycflights13'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RBGL'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'calibration.Rmd' using rmarkdown
Quitting from lines 25-34 (calibration.Rmd) 
Error: processing vignette 'calibration.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'calibration.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'MplusAutomation'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'miceadds'

Packages which this enhances but not available for checking:
  'Hmisc', 'intsvy', 'LSAmitR', 'svyPVpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'haplo.stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bigstatsr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'pillar', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'operations.Rmd' using rmarkdown
--- finished re-building 'operations.Rmd'

--- re-building 'precision.Rmd' using rmarkdown
Quitting from lines 25-27 (precision.Rmd) 
Error: processing vignette 'precision.Rmd' failed with diagnostics:
there is no package called 'pillar'
--- failed re-building 'precision.Rmd'

--- re-building 'type-hierarchy.Rmd' using rmarkdown
--- finished re-building 'type-hierarchy.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'googleAuthR', 'googleCloudStorageR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gargle', 'tibble'

Packages suggested but not available for checking:
  'DBItest', 'dbplyr', 'dplyr', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bigstatsr', 'ggplot2'

Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'gaston', 'Hmisc', 'pcadapt', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cowplot', 'ggplot2', 'tibble'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'testthat'
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'binom-Ex.R' failed
The error most likely occurred in:

> ### Name: binom.bayes
> ### Title: Binomial confidence intervals using Bayesian inference
> ### Aliases: binom.bayes binom.bayes.densityplot
> ### Keywords: univar htest models
> 
> ### ** Examples
> 
> # Example using highest probability density.
> hpd <- binom.bayes(
+   x = 0:10, n = 10, type = "highest", conf.level = 0.8, tol = 1e-9)
> print(hpd)
   method  x  n shape1 shape2       mean       lower     upper sig
1   bayes  0 10    0.5   10.5 0.04545455 0.000000000 0.0769566 0.2
2   bayes  1 10    1.5    9.5 0.13636364 0.003771457 0.2145408 0.2
3   bayes  2 10    2.5    8.5 0.22727273 0.053633312 0.3494770 0.2
4   bayes  3 10    3.5    7.5 0.31818182 0.127646004 0.4728042 0.2
5   bayes  4 10    4.5    6.5 0.40909091 0.214091147 0.5858428 0.2
6   bayes  5 10    5.5    5.5 0.50000000 0.309892028 0.6901080 0.2
7   bayes  6 10    6.5    4.5 0.59090909 0.414157185 0.7859089 0.2
8   bayes  7 10    7.5    3.5 0.68181818 0.527195809 0.8723540 0.2
9   bayes  8 10    8.5    2.5 0.77272727 0.650522982 0.9463667 0.2
10  bayes  9 10    9.5    1.5 0.86363636 0.785459228 0.9962285 0.2
11  bayes 10 10   10.5    0.5 0.95454545 0.923043403 1.0000000 0.2
> binom.bayes.densityplot(hpd)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Error in binom.bayes.densityplot(hpd) : require(ggplot2) is not TRUE
Calls: binom.bayes.densityplot -> stopifnot
Execution halted
Namespace in Imports field not imported from: 'gtools'
  All declared Imports should be used.
Packages required but not available:
  'Rsamtools', 'GenomicAlignments', 'csaw'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'dplyr', 'tibble', 'RcppParallel', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'rstantools', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'msa'
Package required but not available: 'cli'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcmdr'

Packages suggested but not available for checking:
  'car', 'ENMeval', 'readxl', 'dplyr', 'sf', 'blockCV'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'biogas_quick_start.Rnw' using knitr
Quitting from lines 263-268 (biogas_quick_start.Rnw) 
Error: processing vignette 'biogas_quick_start.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'biogas_quick_start.Rnw'

--- re-building 'calcBgMan_function.Rnw' using knitr
Quitting from lines 180-187 (calcBgMan_function.Rnw) 
Error: processing vignette 'calcBgMan_function.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'calcBgMan_function.Rnw'

--- re-building 'calcBgVol_function.Rnw' using knitr
Quitting from lines 145-152 (calcBgVol_function.Rnw) 
Error: processing vignette 'calcBgVol_function.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'calcBgVol_function.Rnw'

--- re-building 'predBg_function.Rnw' using knitr
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'predBg_function.Rnw'

SUMMARY: processing the following files failed:
  'biogas_quick_start.Rnw' 'calcBgMan_function.Rnw'
  'calcBgVol_function.Rnw'

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

> ### Name: plot.criterion_distribution
> ### Title: Plot criterion distribution
> ### Aliases: plot.criterion_distribution
> 
> ### ** Examples
> 
> target_feature <- create_feature_target(10, 375, 15, 600) 
> example_result <- distr_crit(target = target_feature[,1], 
+                              feature = target_feature[,2])
> plot(example_result)
> 
> # a ggplot2 plot
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'overview.Rmd' using rmarkdown
Loading required package: slam
Quitting from lines 16-40 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'tibble', 'dplyr', 'ggplot2', 'cowplot', 'lamW', 'tidyr'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'biomaRt'
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'mice', 'ggplot2', 'tidyr', 'mitml'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'lintr'
Packages required but not available:
  'biomaRt', 'tibble', 'dplyr', 'readr', 'philentropy'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'sf'
Packages required but not available: 'ChemmineR', 'fmcsR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'caret', 'ENMeval', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'Hmisc', 'testthat', 'ecospat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bioinactivation', 'dplyr', 'ggplot2', 'MEIGOR', 'tidyr', 'tidyverse'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'factoextra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'ggmap', 'ggplot2', 'rhdf5', 'tidyr', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'pillar', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'dplyr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', 'plsRcox'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

Packages suggested but not available for checking:
  'bshazard', 'Epi', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'car'
Packages suggested but not available for checking:
  'soilphysics', 'SpatialEpi'
Package required but not available: 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: 'bipartite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sna', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'matlib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'ggplot2', 'ggrepel'
Running examples in 'BiplotML-Ex.R' failed
The error most likely occurred in:

> ### Name: gradientDesc
> ### Title: Gradient function for Binary Logistic Biplot
> ### Aliases: gradientDesc
> 
> ### ** Examples
> 
> data('Methylation')
> set.seed(02052020)
> MatGD <- gradientDesc(x = Methylation, k=2, max_iter=10000)
[1] "The process converge with 220 iterations"
> outGD <- gradientDesc(x = Methylation, k=2, max_iter=10000, plot = TRUE)
[1] "The process converge with 182 iterations"
Error: Package "tidyr" needed for this function to work. Please install it.
Execution halted
Package suggested but not available for checking: 'sampleSelection'
Running examples in 'BiProbitPartial-Ex.R' failed
The error most likely occurred in:

> ### Name: BiProbitPartial
> ### Title: Bivariate probit with partial observability
> ### Aliases: BiProbitPartial
> 
> ### ** Examples
> 
> data('Mroz87',package = 'sampleSelection')
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'sampleSelection'
Calls: data -> find.package
Execution halted
Package required but not available: 'rworldmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'sf', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'bisect_vignette.Rmd' using rmarkdown
Quitting from lines 69-101 (bisect_vignette.Rmd) 
Error: processing vignette 'bisect_vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'bisect_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'fields'
Running examples in 'bisque-Ex.R' failed
The error most likely occurred in:

> ### Name: sFit
> ### Title: Fit a spatially mean-zero spatial Gaussian process model
> ### Aliases: sFit
> 
> ### ** Examples
> 
> library(fields)
Error in library(fields) : there is no package called 'fields'
Execution halted
Packages suggested but not available for checking: 'Seurat', 'testthat'
Packages required but not available: 'dplyr', 'readr', 'tidyr', 'rvest'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'httptest', 'testthat', 'tidyquant'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'corrgram' 'rpivotTable' 'shinyAce'
  All declared Imports should be used.
Package suggested but not available for checking: 'mrfDepth'
Package required but not available: 'fields'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bkmr', 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'fields', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'ggExtra'
Error(s) in re-building vignettes:
--- re-building 'Intro.Rmd' using knitr
Quitting from lines 72-75 (Intro.Rmd) 
Error: processing vignette 'Intro.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'basecamb', 'Hmisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'bayesplot', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'ggplot2', 'cowplot', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'arm'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'devtools', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Package suggested but not available for checking: 'nbpMatching'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'caret', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'ggplot2', 'forecast', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'edstan', 'ggplot2', 'GGUM',
  'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'ggplot2', 'StanHeaders'

Packages suggested but not available for checking: 'qgraph', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'readr', 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'bayesplot', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'mlr', 'testthat'
Package unavailable to check Rd xrefs: 'mlr'
Packages required but not available: 'dplyr', 'factormodel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'qgraph', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pec'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'bnormnlr-Ex.R' failed
The error most likely occurred in:

> ### Name: bnlr
> ### Title: Bayesian Estimation for Normal Heteroscedastic Nonlinear
> ###   Regression Models.
> ### Aliases: bnlr
> 
> ### ** Examples
> 
> 
> ######################################################
> ###Simulation of heteroscedastic model, using gradient
> ######################################################
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Packages required but not available: 'fastDummies', 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'viridis'

Packages suggested but not available for checking: 'testthat', 'BNPmix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'qgraph', 'testthat'
Packages suggested but not available for checking:
  'ggplot2', 'cytofan', 'dplyr'
Error(s) in re-building vignettes:
--- re-building 'bodenmiller.Rmd' using rmarkdown
Quitting from lines 13-24 (bodenmiller.Rmd) 
Error: processing vignette 'bodenmiller.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'bodenmiller.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'tibble'
Package required but not available: 'styler'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'testthat'
Package required but not available: 'randomForestSRC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'intergraph', 'GGally', 'network', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'pkgdown', 'devtools', 'mockery'
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Namespaces in Imports field not imported from:
  'HSAUR3' 'knitr' 'rmarkdown'
  All declared Imports should be used.
Package required but not available: 'mice'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'IsingFit', 'qgraph', 'dplyr', 'tidyr', 'IsingSampler',
  'mgm', 'NetworkToolbox', 'graphicalVAR', 'networktools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plsRglm', 'bipartite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'doMC', 'qvalue', 'testthat'
Package unavailable to check Rd xrefs: 'qvalue'
Error(s) in re-building vignettes:
--- re-building 'bootUR-intro.Rmd' using rmarkdown
Quitting from lines 74-75 (bootUR-intro.Rmd) 
Error: processing vignette 'bootUR-intro.Rmd' failed with diagnostics:
Cannot plot missing values as package ggplot2 not installed.
--- failed re-building 'bootUR-intro.Rmd'

SUMMARY: processing the following file failed:
  'bootUR-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'borrowr-package.Rmd' using rmarkdown
Quitting from lines 36-42 (borrowr-package.Rmd) 
Error: processing vignette 'borrowr-package.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'borrowr-package.Rmd'

SUMMARY: processing the following file failed:
  'borrowr-package.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'cplexAPI', 'testthat', 'ggplot2', 'ggpubr', 'dplyr', 'kableExtra',
  'devtools', 'bestsubset'
Error(s) in re-building vignettes:
--- re-building 'BOSO.Rmd' using rmarkdown
Quitting from lines 21-29 (BOSO.Rmd) 
Error: processing vignette 'BOSO.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'BOSO.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'devtools', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'BOSSreg.Rmd' using rmarkdown
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Quitting from lines 308-333 (BOSSreg.Rmd) 
Error: processing vignette 'BOSSreg.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'BOSSreg.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'qicharts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Needed for subshells openend in tests, and does no harm otherwise.
  > # See <https://github.com/hadley/testthat/issues/144> for details.
  > Sys.setenv(R_TESTS = '')
  > testthat::test_check('box')
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'dplyr', 'rio', 'tibble'

Packages suggested but not available for checking:
  'gargle', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'bpbounds.Rmd' using rmarkdown
Quitting from lines 36-39 (bpbounds.Rmd) 
Error: processing vignette 'bpbounds.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'bpbounds.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'RcppParallel', 'rstan', 'rstantools',
  'tibble', 'shinystan', 'badger', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'bayesplot', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'fields', 'OpenStreetMap', 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fabMix'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'cowplot', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'NPflow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geojsonio', 'rgbif', 'rworldmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Hmisc', 'car', 'ggplot2', 'ggrepel', 'mediation'
Packages unavailable to check Rd xrefs: 'Hmisc', 'car', 'mediation'
Package required but not available: 'CCA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'readxl', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'caret', 'DALEX', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggfittext', 'ggplot2', 'broom', 'readr', 'readxl',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'breathteststan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rstan', 'rstantools', 'tibble', 'tidyr', 'StanHeaders'

Packages suggested but not available for checking:
  'ggplot2', 'shinystan', 'bayesplot', 'testthat', 'breathtestcore'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'detectseparation', 'testthat'
Package unavailable to check Rd xrefs: 'detectseparation'
Error(s) in re-building vignettes:
--- re-building 'adjacent.Rmd' using rmarkdown
--- finished re-building 'adjacent.Rmd'

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

--- re-building 'multinomial.Rmd' using rmarkdown
Quitting from lines 83-86 (multinomial.Rmd) 
Error: processing vignette 'multinomial.Rmd' failed with diagnostics:
there is no package called 'detectseparation'
--- failed re-building 'multinomial.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'the_bridgedist_basics.Rmd' using rmarkdown
Quitting from lines 33-45 (the_bridgedist_basics.Rmd) 
Error: processing vignette 'the_bridgedist_basics.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'the_bridgedist_basics.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'plotly'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'rstan', 'rstanarm'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'tibble', 'forcats', 'GGally'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'httptest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'testthat'

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Rcpp' 'profileModel'
  All declared Imports should be used.
Packages required but not available:
  'rstan', 'ggplot2', 'rstantools', 'bayesplot', 'shinystan',
  'projpred'

Packages suggested but not available for checking:
  'testthat', 'cmdstanr', 'mice', 'spdep', 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'mice', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'broom.mixed', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cli', 'dplyr', 'labelled', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'forcats', 'geepack', 'ggplot2', 'gt',
  'gtsummary', 'mice', 'rstanarm', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'dotwhisker', 'testthat', 'ggplot2', 'glmmADMB', 'lmerTest',
  'pbkrtest', 'rstan', 'rstanarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'AER', 'btergm', 'car', 'caret', 'drc', 'ergm', 'geepack', 'ggplot2',
  'Hmisc', 'joineRML', 'Lahman', 'mediation', 'mlogit', 'modeltests',
  'network', 'rsample', 'spdep', 'spatialreg', 'systemfit', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'benchmarks.Rmd' using rmarkdown
Quitting from lines 24-36 (benchmarks.Rmd) 
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'benchmarks.Rmd'

--- re-building 'brotli-2015-09-22.pdf.asis' using asis
--- finished re-building 'brotli-2015-09-22.pdf.asis'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'taxize', 'phylocomr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jmv', 'ggplot2', 'ggtext', 'cowplot', 'see'

Packages suggested but not available for checking:
  'rio', 'dplyr', 'tidyr', 'forcats', 'car', 'afex', 'mediation',
  'interactions', 'jtools', 'lmerTest', 'GGally'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BRugs/BRugs.Rcheck/00install.out' for details.
Packages required but not available: 'DiffBind', 'Rsamtools', 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'usage.Rmd' using rmarkdown
Quitting from lines 59-63 (usage.Rmd) 
Error: processing vignette 'usage.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'usage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'blavaan', 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'golem', 'thematic', 'echarts4r'
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'sf', 'spdep'
Error(s) in re-building vignettes:
--- re-building 'vulnerability_in_dar.Rmd' using rmarkdown
Quitting from lines 28-31 (vulnerability_in_dar.Rmd) 
Error: processing vignette 'vulnerability_in_dar.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building 'vulnerability_in_dar.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr'
Packages required but not available:
  'viridis', 'rstan', 'rstantools', 'DiagrammeR', 'StanHeaders'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat', 'bayesplot', 'tidybayes',
  'ggplot2', 'ggfortify', 'plotly', 'ggridges', 'visdat', 'tidyr',
  'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Epi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'thematic', 'testthat'
Package required but not available: 'diagis'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'Hmisc', 'sde', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ClusterR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (requireNamespace("BSW")) {
  +   library(BSW)
  +   library(testthat)
  +   test_check("BSW")
  + }
  Loading required namespace: BSW
  Loading required package: Matrix
  Loading required package: matrixStats
  Loading required package: quadprog
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Validation.Rmd' using rmarkdown
Quitting from lines 28-37 (Validation.Rmd) 
Error: processing vignette 'Validation.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'Validation.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sf', 'RcppParallel'

Package suggested but not available for checking: 'cartography'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'network', 'sna', 'ergm'

Packages suggested but not available for checking:
  'testthat', 'Bergm', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggforce'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BTYD'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mice'
Package unavailable to check Rd xrefs: 'mice'
Package required but not available: 'sf'

Package suggested but not available for checking: 'openair'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'lmerTest', 'pbkrtest', 'testthat'
Packages required but not available: 'usethis', 'readr', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'ldatuning'
Packages required but not available: 'dplyr', 'Hmisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'broom', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forcats', 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'Hmisc', 'testthat'
Packages required but not available: 'tibble', 'usethis'

Packages suggested but not available for checking:
  'caret', 'dplyr', 'flexsurv', 'NMF', 'parsnip', 'pkgload', 'recipes',
  'rsample', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'riskRegression', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright 2016 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of BWStest.
  > #
  > # BWStest is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # BWStest is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with BWStest.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2016.03.25
  > # Copyright: Steven E. Pav, 2016-2016
  > # Author: Steven E. Pav
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggforce', 'ggrepel', 'multichull', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dynlm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FactoMineR', 'ggplot2', 'ggrepel', 'Hmisc', 'RcmdrMisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  w32-backend.c:24:5: warning: initialization of 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Cairo/Cairo.Rcheck/00install.out' for details.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'smoof', 'car', 'dplyr', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'taxize', 'dendextend', 'heatmaply', 'ggplot2', 'plotly', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'forcats', 'ggimage', 'gggibbous'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ReGenesees', 'testthat'
Packages required but not available: 'ggplot2', 'rworldmap'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'cli', 'testthat'
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'secr'

Packages suggested but not available for checking:
  'ritis', 'taxize', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'leaflet', 'readr', 'sf', 'tidyr', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'systemfit', 'qvalue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', 'dplyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'heplots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'rvest', 'tibble'

Packages suggested but not available for checking:
  'tidyr', 'ggplot2', 'dbplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'tibble', 'tidyr', 'usethis'
Packages suggested but not available for checking:
  'dplyr', 'readr', 'testthat', 'tibble', 'tidyr'
Running 'ci-tests.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'GGally', 'leaflet', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'GGally', 'ggplot2', 'leaflet', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rtweet'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'car'
Packages required but not available:
  'sf', 'ggplot2', 'tidyr', 'dplyr', 'tibble', 'readr', 'broom',
  'hardhat', 'recipes', 'Hmisc', 'ggrepel'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'caret'

Packages suggested but not available for checking:
  'testthat', 'lintr', 'klaR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'recipes'

Packages suggested but not available for checking:
  'klaR', 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggraph', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'CarletonStats-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedBar
> ### Title: Grouped bar chart
> ### Aliases: groupedBar groupedBar.default groupedBar.formula
> ### Keywords: bar grouped plot
> 
> ### ** Examples
> 
> 
> 
> groupedBar(states03$Region)
Error in groupedBar.default(states03$Region) : 
  ggplot2 packaged needed for this function to work.
Calls: groupedBar -> groupedBar.default
Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DESeq2', 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pbkrtest', 'rio'

Package suggested but not available for checking: 'alr4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'plotly', 'sf'

Packages suggested but not available for checking:
  'testthat', 'cartography'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'lwgeom', 'SpatialPosition'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'dplyr', 'gapminder', 'ggplot2', 'roxygen2', 'sde',
  'tidyverse', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'abind'
  All declared Imports should be used.
Package required but not available: 'Hmisc'

Packages suggested but not available for checking: 'expsmooth', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'haven', 'labelled', 'tidyr', 'tibble', 'janitor', 'srvyr'

Packages suggested but not available for checking: 'testthat', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bipartite', 'dplyr', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'ggplot2'

Packages suggested but not available for checking:
  'mapview', 'sf', 'virtualspecies', 'viridis', 'stars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'tidyr', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sparklyr'

Packages suggested but not available for checking: 'pkgdown', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rms', 'mlogit', 'Ecdat', 'geepack', 'GAMBoost'
Packages required but not available:
  'ggplot2', 'tidyverse', 'dplyr', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
Packages required but not available: 'ruv', 'sva', 'leapp'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'Hmisc', 'broom'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'spacodiR', 'entropart', 'mice'
Packages required but not available: 'season', 'assertr', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'tidyverse', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'Epi', 'verification', 'Hmisc'
Package required but not available: 'testthat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mlogit'
Package unavailable to check Rd xrefs: 'mlogit'
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'lintr', 'nycflights13', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DiagrammeR', 'dplyr', 'ggplot2', 'tidyr', 'cowplot', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyverse', 'ggalt', 'cobalt', 'ggsci', 'naniar', 'Hmisc',
  'hrbrthemes', 'summarytools', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'cmp_rsk_RHC.Rmd' using rmarkdown
Quitting from lines 302-325 (cmp_rsk_RHC.Rmd) 
Error: processing vignette 'cmp_rsk_RHC.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'cmp_rsk_RHC.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'Hmisc', 'testthat', 'tidyr'
Package required but not available: 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rstan', 'rstantools', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'hdm', 'fastDummies'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggforce', 'ggrepel', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'tidyr', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'prettydoc'
  All declared Imports should be used.
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'DiagrammeR'
Packages required but not available: 'haven', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'GeneNet'
  All declared Imports should be used.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'lsbclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Packages suggested but not available for checking: 'testthat', 'nnTensor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'dplyr', 'readxl', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ddpcr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GDINA', 'ggplot2', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'sf', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds'

Package which this enhances but not available for checking: 'GDINA'
Packages unavailable to check Rd xrefs: 'GDINA', 'car'
Packages required but not available: 'GDINA', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'broom'

Package suggested but not available for checking: 'eemR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'freqparcoord'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Seurat', 'ggplot2', 'dplyr', 'ggpubr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'dendextend', 'ggplot2', 'ggbeeswarm'
Error(s) in re-building vignettes:
--- re-building 'QC.Rmd' using rmarkdown
Quitting from lines 26-28 (QC.Rmd) 
Error: processing vignette 'QC.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'QC.Rmd'

--- re-building 'ana-methods.Rmd' using rmarkdown
Quitting from lines 23-25 (ana-methods.Rmd) 
Error: processing vignette 'ana-methods.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ana-methods.Rmd'

--- re-building 'clustering.Rmd' using rmarkdown
Quitting from lines 164-167 (clustering.Rmd) 
Error: processing vignette 'clustering.Rmd' failed with diagnostics:
clusterTracks: please install the 'dendextend' package to use this functionality!
--- failed re-building 'clustering.Rmd'

--- re-building 'reading-converting-data.Rmd' using rmarkdown
Quitting from lines 21-23 (reading-converting-data.Rmd) 
Error: processing vignette 'reading-converting-data.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'reading-converting-data.Rmd'

--- re-building 'simulation.Rmd' using rmarkdown
Quitting from lines 27-29 (simulation.Rmd) 
Error: processing vignette 'simulation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'simulation.Rmd'

SUMMARY: processing the following files failed:
  'QC.Rmd' 'ana-methods.Rmd' 'clustering.Rmd'
  'reading-converting-data.Rmd' 'simulation.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'robustHD', 'rospca', 'GSE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidycensus', 'sf', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'cli'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'dbplyr', 'chilemapas'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'AER'
Packages unavailable to check Rd xrefs: 'AER', 'sampleSelection'
Running examples in 'censReg-Ex.R' failed
The error most likely occurred in:

> ### Name: censReg
> ### Title: Censored Regression (Tobit) Model
> ### Aliases: censReg print.censReg
> ### Keywords: models regression
> 
> ### ** Examples
> 
> ## Kleiber & Zeileis ( 2008 ), page 142
> data( "Affairs", package = "AER" )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Running 'censRegFail.R'
Running the tests in 'tests/censRegFail.R' failed.
Complete output:
  > library( "censReg" )
  Loading required package: maxLik
  Loading required package: miscTools
  
  Please cite the 'maxLik' package as:
  Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.
  
  If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
  https://r-forge.r-project.org/projects/maxlik/
  
  Please cite the 'censReg' package as:
  Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.
  
  If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
  https://r-forge.r-project.org/projects/sampleselection/
  > 
  > data( "Affairs", package = "AER" )
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'AER'
  Calls: data -> find.package
  Execution halted
Errors in running code in vignettes:
when running code in 'censReg.Rnw'

> options(prompt = "R> ", ctinue = "+  ")

> library("censReg")
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Please cite the 'censReg' package as:
Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.

If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
https://r-forge.r-project.org/projects/sampleselection/

> data("Affairs", package = "AER")

  When sourcing 'censReg.R':
Error: there is no package called 'AER'
Execution halted

  'censReg.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'censReg.Rnw' using Sweave
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Please cite the 'censReg' package as:
Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.

If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
https://r-forge.r-project.org/projects/sampleselection/

Error: processing vignette 'censReg.Rnw' failed with diagnostics:
 chunk 3 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'

--- failed re-building 'censReg.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'testthat'
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'Census2016.Rmd' using rmarkdown
Quitting from lines 63-74 (Census2016.Rmd) 
Error: processing vignette 'Census2016.Rmd' failed with diagnostics:
object '.CensusDataTables' not found
--- failed re-building 'Census2016.Rmd'

SUMMARY: processing the following file failed:
  'Census2016.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'sf', 'testthat'
Package required but not available: 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gravity'
Packages required but not available: 'tibble', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'spex'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'DALEX'

Packages suggested but not available for checking: 'ggiraph', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Hmisc', 'randomForestSRC'
Packages required but not available: 'fda', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'mockery', 'testthat'
Running 'runTests.R'
Running the tests in 'tests/runTests.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running examples in 'CGGP-Ex.R' failed
The error most likely occurred in:

> ### Name: CGGPplotblockselection
> ### Title: Plot CGGP block selection over time
> ### Aliases: CGGPplotblockselection
> 
> ### ** Examples
> 
> gs <- CGGPcreate(d=3, batchsize=100)
> # All dimensions will look similar
> CGGPplotblockselection(gs)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: CGGPplotblockselection ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'CGGP.Rmd' using rmarkdown
Quitting from lines 178-179 (CGGP.Rmd) 
Error: processing vignette 'CGGP.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'CGGP.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'readxl', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyverse', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggmosaic', 'ggplot2', 'ggrepel', 'paletteer',
  'sjstats', 'tidyr'

Packages suggested but not available for checking:
  'ggthemes', 'hrbrthemes', 'janitor', 'productplots', 'tibble',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright 2020 Ron Triepels
  > #
  > # Licensed under the Apache License, Version 2.0 (the "License");
  > # you may not use this file except in compliance with the License.
  > # You may obtain a copy of the License at
  > #
  > #    http://www.apache.org/licenses/LICENSE-2.0
  > #
  > # Unless required by applicable law or agreed to in writing, software
  > # distributed under the License is distributed on an "AS IS" BASIS,
  > # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > # See the License for the specific language governing permissions and
  > # limitations under the License.
  > 
  > library(cgraph)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Hmisc', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'dplyr', 'sf'
Packages required but not available: 'systemfit', 'cplm', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'bench', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'available', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'iptools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'textreadr'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'ggplot2', 'tidygraph', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-CheckDigit.R'
Running the tests in 'tests/test-CheckDigit.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'testthat', 'tibble'
Running examples in 'checkmate-Ex.R' failed
The error most likely occurred in:

> ### Name: checkTibble
> ### Title: Check if an argument is a tibble
> ### Aliases: checkTibble check_tibble assertTibble assert_tibble testTibble
> ###   test_tibble expect_tibble
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called 'tibble'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'checkmate.Rmd' using rmarkdown
Quitting from lines 160-171 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'checkmate.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'pkgdepends'

Packages suggested but not available for checking: 'pkgcache', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'kableExtra', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'mlrMBO', 'smoof', 'mlr'
Packages suggested but not available for checking: 'speaq', 'hyperSpec'
Running examples in 'ChemoSpec-Ex.R' failed
The error most likely occurred in:

> ### Name: clupaSpectra
> ### Title: Hierarchical Cluster-Based Peak Alignment on a Spectra Object
> ### Aliases: clupaSpectra
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> data(alignMUD)
> 
> plotSpectra(alignMUD,
+   which = 1:20, lab.pos = 4.5, offset = 0.1,
+   yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
+   main = "Misaligned NMR Spectra (alignMUD)"
+ )
> 
> aMUD <- clupaSpectra(alignMUD)
Error in clupaSpectra(alignMUD) : 
  You need to install package speaq to use this function
Execution halted
Package suggested but not available for checking: 'roxut'
Running examples in 'cherryblossom-Ex.R' failed
The error most likely occurred in:

> ### Name: run09
> ### Title: Cherry Blossom Run data, 2009
> ### Aliases: run09
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages required but not available: 'broom', 'ggplot2', 'tibble', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bedr'

Packages suggested but not available for checking:
  'testthat', 'GenomicInteractions', 'Gviz', 'countreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bigstatsr', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'purrrlyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'rmapshaper', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'chillR', 'dplyr', 'ggplot2'
Package unavailable to check Rd xrefs: 'chillR'
Packages required but not available: 'dplyr', 'fields', 'readxl', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bruceR'

Packages suggested but not available for checking: 'babynames', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'drc', 'RDML', 'testthat'
Running examples in 'chk-Ex.R' failed
The error most likely occurred in:

> ### Name: expect_chk_error
> ### Title: Expect Chk Error
> ### Aliases: expect_chk_error
> 
> ### ** Examples
> 
> expect_chk_error(chk_true(FALSE))
Error in expect_chk_error(chk_true(FALSE)) : `testhat` must be installed.
Execution halted
Packages required but not available:
  'Hmisc', 'ggplot2', 'dplyr', 'ggmap', 'tigris', 'rvest', 'tidyr',
  'tidycensus'

Packages suggested but not available for checking:
  'testthat', 'choroplethrAdmin1'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rvest', 'forcats'

Packages suggested but not available for checking:
  'ggplot2', 'network', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'readr', 'skimr', 'viridis'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'readxl', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'dbplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'stringr'
  All declared Imports should be used.
Running 'test_cif.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'fields'

Packages suggested but not available for checking:
  'ggplot2', 'ggpubr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'twang', 'arm', 'dplyr', 'car', 'WeightIt', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ChIPseeker', 'DESeq2', 'dplyr', 'fgsea', 'ggplot2', 'ggrepel',
  'sva', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

Package suggested but not available for checking: 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'network', 'sna', 'FactoMineR', 'factoextra', 'GGally', 'dendextend',
  'viridis', 'ggplot2', 'intergraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cli'

Packages suggested but not available for checking:
  'gh', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dendextend'
Running examples in 'circlize-Ex.R' failed
The error most likely occurred in:

> ### Name: circos.dendrogram
> ### Title: Add circular dendrograms
> ### Aliases: circos.dendrogram
> 
> ### ** Examples
> 
> load(system.file(package = "circlize", "extdata", "bird.orders.RData"))
> 
> labels = hc$labels  # name of birds
> ct = cutree(hc, 6)  # cut tree into 6 pieces
> n = length(labels)  # number of bird species
> dend = as.dendrogram(hc)
> 
> circos.par(cell.padding = c(0, 0, 0, 0))
> circos.initialize(sectors = "a", xlim = c(0, n)) # only one sector
> max_height = attr(dend, "height")  # maximum height of the trees
> circos.trackPlotRegion(ylim = c(0, 1), bg.border = NA, track.height = 0.3,
+     panel.fun = function(x, y) {
+         for(i in seq_len(n)) {
+             circos.text(i-0.5, 0, labels[i], adj = c(0, 0.5),
+                 facing = "clockwise", niceFacing = TRUE,
+                 col = ct[labels[i]], cex = 0.7)
+         }
+ })
> 
> suppressPackageStartupMessages(require(dendextend))
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dendextend'
> dend = color_branches(dend, k = 6, col = 1:6)
Error in color_branches(dend, k = 6, col = 1:6) : 
  could not find function "color_branches"
Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'plotly', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggrepel', 'kableExtra', 'roxygen2', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'arm', 'dplyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dataRetrieval', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'feather', 'ggplot2', 'roxygen2', 'mockery', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'civis_ml.Rmd' using rmarkdown
Quitting from lines 215-216 (civis_ml.Rmd) 
Error: processing vignette 'civis_ml.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'civis_ml.Rmd'

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'cregg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dbplyr'

Packages suggested but not available for checking:
  'sf', 'readxl', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # testthat.R -- automated test cases
  > #
  > # MS
  > # Created: Feb 8, 2015
  > 
  > require("testthat")
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require("Ckmeans.1d.dp")
  Loading required package: Ckmeans.1d.dp
  > 
  > test_check("Ckmeans.1d.dp")
  Error in test_check("Ckmeans.1d.dp") : 
    could not find function "test_check"
  Execution halted
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'ggraph', 'readr', 'tibble',
  'tidygraph', 'tidyr', 'vroom'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'caret'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'cellWise'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'readtext'
Found the following significant warnings:
  WARNING: failed to apply patch patches/CRAN/cld3.diff
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cld3/cld3.Rcheck/00install.out' for details.
Package required but not available: 'pillar'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cleaner'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pkgload'

Packages suggested but not available for checking:
  'devtools', 'rasciidoc', 'testthat', 'usethis'

VignetteBuilder package required for checking but not installed: 'rasciidoc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rvest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'ggplot2', 'ggpubr', 'ggthemes',
  'gganimate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr'
Package suggested but not available for checking: 'rangeBuilder'
Package suggested but not available for checking: 'fields'
Packages suggested but not available for checking:
  'MODISTools', 'nasapower', 'sf', 'testthat'
Package required but not available: 'SPEI'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clinUtils', 'ggplot2', 'haven', 'plotly'

Packages suggested but not available for checking:
  'inTextSummaryTable', 'patientProfilesVis', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'ggplot2', 'tibble', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'ggplot2', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'haven'

Packages suggested but not available for checking:
  'dplyr', 'tibble', 'ggplot2', 'plotly', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mockery', 'testthat', 'tibble'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cli/cli.Rcheck/00install.out' for details.
Packages required but not available: 'ggplot2', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'geepack', 'AER', 'testthat'
Running examples in 'clubSandwich-Ex.R' failed
The error most likely occurred in:

> ### Name: vcovCR.glm
> ### Title: Cluster-robust variance-covariance matrix for a glm object.
> ### Aliases: vcovCR.glm
> 
> ### ** Examples
> 
> 
> data(dietox, package = "geepack")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'geepack'
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Wald-tests-in-clubSandwich.Rmd' using rmarkdown
Registered S3 method overwritten by 'clubSandwich':
  method    from    
  bread.mlm sandwich
Quitting from lines 22-32 (Wald-tests-in-clubSandwich.Rmd) 
Error: processing vignette 'Wald-tests-in-clubSandwich.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building 'Wald-tests-in-clubSandwich.Rmd'

--- re-building 'meta-analysis-with-CRVE.Rmd' using rmarkdown
Loading required package: Matrix

Loading the 'metafor' package (version 3.0-2). For an
introduction to the package please type: help(metafor)

--- finished re-building 'meta-analysis-with-CRVE.Rmd'

--- re-building 'panel-data-CRVE.Rmd' using rmarkdown
--- finished re-building 'panel-data-CRVE.Rmd'

SUMMARY: processing the following file failed:
  'Wald-tests-in-clubSandwich.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tableone'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'dendextend', 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggfortify', 'npregfast'

Packages suggested but not available for checking: 'testthat', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qrcm', 'fda', 'ggpubr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'GSVA', 'singscore', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'dplyr', 'roxygen2', 'testthat'
Namespaces in Imports field not imported from:
  'R6' 'methods' 'purrr'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Quitting from lines 144-151 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
1/1 jobs failed (0 warnings). Stopping.
(Error #1) there is no package called 'dplyr'
--- failed re-building 'quickstart.Rmd'

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

--- re-building 'userguide.Rmd' using rmarkdown
Quitting from lines 208-214 (userguide.Rmd) 
Error: processing vignette 'userguide.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'userguide.Rmd'

SUMMARY: processing the following files failed:
  'quickstart.Rmd' 'userguide.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'using-clusternomics.Rmd' using rmarkdown
Quitting from lines 37-42 (using-clusternomics.Rmd) 
Error: processing vignette 'using-clusternomics.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'using-clusternomics.Rmd'

SUMMARY: processing the following file failed:
  'using-clusternomics.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'car', 'dendextend'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'car', 'lmerTest'

Packages suggested but not available for checking:
  'geepack', 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'AER', 'mlogit', 'dfidx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'WeightedCluster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ClusterR', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'ggExtra', 'testthat', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'tidyverse', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'GGally', 'dplyr', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggraph', 'dplyr', 'ggplot2', 'viridis', 'tidygraph', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'Seurat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'tidygraph', 'ggraph', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'klaR', 'dplyr', 'psycho'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'VarSelLCM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'smoof', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'testthat', 'usethis'

Package suggested but not available for checking: 'cli'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'cmfrec_vignette.Rmd' using rmarkdown
'MatrixExtra' modifies important behaviors from 'Matrix'. See ?MatrixExtra-options.
Loading required package: arules

Attaching package: 'arules'

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

    abbreviate, write

Loading required package: proxy

Attaching package: 'proxy'

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

    as.matrix

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

    as.dist, dist

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

    as.matrix

Loading required package: registry
Quitting from lines 347-363 (cmfrec_vignette.Rmd) 
Error: processing vignette 'cmfrec_vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'cmfrec_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'
Packages required but not available: 'ggplot2', 'twang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Packages suggested but not available for checking:
  'cmsaf', 'cmsafvis', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cmsafops', 'cmsafvis', 'colourpicker', 'fields', 'shinyFiles'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cmsafops', 'fields'

Packages suggested but not available for checking:
  'plotKML', 'rnaturalearth', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'rvest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'lintr', 'testthat', 'tidyr', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readxl', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cna', 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'readxl', 'testthat'
Packages required but not available:
  'rstan', 'rstantools', 'RcppParallel', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'GenomicInteractions', 'biomaRt', 'dplyr',
  'rtracklayer'

Packages suggested but not available for checking:
  'plotly', 'GenomicFeatures', 'heatmaply',
  'BSgenome.Hsapiens.UCSC.hg19', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'tidyr', 'dplyr', 'ggplot2', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'WeightIt', 'twang', 'optweight', 'mice', 'MatchThem', 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'ggplot2', 'ggtern', 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'

Package which this enhances but not available for checking: 'rkward'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in testthat/test.r
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running 'test.cocron.package.R'
Running the tests in 'tests/test.cocron.package.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ../inst/tests
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_package("cocron")
  Error in test_package("cocron") : could not find function "test_package"
  Execution halted
Packages required but not available:
  'forcats', 'ggplot2', 'dplyr', 'tidyr', 'haven', 'tibble', 'likert',
  'skimr', 'labelled'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'roxygen2', 'rio', 'ufs',
  'userfriendlyscience'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'kableExtra', 'readr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'REDCapR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'car', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'codingMatrices.Rnw' using knitr
Quitting from lines 19-30 (codingMatrices.Rnw) 
Error: processing vignette 'codingMatrices.Rnw' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'codingMatrices.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'pillar', 'devtools', 'dplyr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat) 
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Community_Stability_Metrics.Rmd' using rmarkdown
--- finished re-building 'Community_Stability_Metrics.Rmd'

--- re-building 'Temporal_Diversity_Indices.Rmd' using rmarkdown
Quitting from lines 108-110 (Temporal_Diversity_Indices.Rmd) 
Error: processing vignette 'Temporal_Diversity_Indices.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Temporal_Diversity_Indices.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'useful', 'dplyr', 'tibble', 'plotly'

Packages suggested but not available for checking:
  'testthat', 'workflows', 'parsnip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ## Test `coenocliner` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'car', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'tidyr', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dtplyr', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Epi', 'ggplot2', 'DiagrammeR'

Packages suggested but not available for checking: 'mstate', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'cli'

Packages suggested but not available for checking:
  'testthat', 'ggthemes', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sf', 'weights', 'dplyr', 'ggplot2', 'testthat'
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tibble'
Packages required but not available: 'network', 'latentnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'viridis', 'susieR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'shinytest', 'devtools'
Packages required but not available: 'ggplot2', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tibble', 'dplyr', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'colorDF.Rmd' using rmarkdown
Quitting from lines 42-45 (colorDF.Rmd) 
Error: processing vignette 'colorDF.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'colorDF.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'plotly'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'pkgdown'
Running examples in 'colorednoise-Ex.R' failed
The error most likely occurred in:

> ### Name: autocorr_sim
> ### Title: Simulate Temporally Autocorrelated Populations for Every
> ###   Combination of Parameters
> ### Aliases: autocorr_sim
> 
> ### ** Examples
> 
> survival_range <- autocorr_sim(timesteps = 30, start = 200, survPhi = 0.3, fecundPhi = 0.1,
+                                survMean = c(0.2, 0.3, 0.4, 0.5, 0.6), survSd = 0.5,
+                                fecundMean = 1.1, fecundSd = 0.5, replicates = 50)
Error: The tibble package must be installed
Backtrace:
    █
 1. ├─colorednoise::autocorr_sim(...)
 2. │ ├─`%>%`(...)
 3. │ └─purrr::cross_df(...)
 4. │   └─purrr:::check_tibble()
 5. └─purrr::rerun(., .n = replicates, pmap(., unstructured_pop))
 6.   └─purrr:::eval_dots(dots)
 7.     └─base::lapply(x, eval_tidy)
 8.       └─rlang:::FUN(X[[i]], ...)
Execution halted
Packages required but not available: 'tibble', 'treemap', 'dplyr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'sf', 'rnaturalearth', 'tigris'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'tibble', 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'rcartocolor', 'viridis'
Running examples in 'colorspace-Ex.R' failed
The error most likely occurred in:

> ### Name: scale_colour_binned_diverging
> ### Title: HCL-Based Binned Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_binned_diverging scale_color_binned_diverging
> ###   scale_fill_binned_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
Error in library("ggplot2") : there is no package called 'ggplot2'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'colorspace.Rmd' using rmarkdown
Quitting from lines 20-24 (colorspace.Rmd) 
Error: processing vignette 'colorspace.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'colorspace.Rmd'

--- re-building 'hcl-colors.Rnw' using Sweave
Loading required package: grid
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'hcl-colors.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'httptest', 'testthat', 'vdiffr'
Namespace in Imports field not imported from: 'crayon'
  All declared Imports should be used.
Packages suggested but not available for checking: 'httptest', 'testthat'
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
Package required but not available: 'adespatial'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GGally', 'useful', 'ggplot2', 'wrassp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'backShift', 'CAM', 'testthat'
Packages required but not available: 'HardyWeinberg', 'kableExtra'

Packages suggested but not available for checking: 'readxl', 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'GGally', 'tibble'
Running examples in 'comparer-Ex.R' failed
The error most likely occurred in:

> ### Name: hype
> ### Title: Hyperparameter optimization
> ### Aliases: hype
> 
> ### ** Examples
> 
> 
> # Have df output, but only use one value from it
> h1 <- hype$new(
+   eval_func = function(a, b) {data.frame(c=a^2+b^2, d=1:2)},
+   extract_output_func = function(odf) {odf$c[1]},
+   a = par_unif$new('a', -1, 2),
+   b = par_unif$new('b', -10, 10),
+   n_lhs = 10
+ )
> h1$run_all()
Running 1, completed 0/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] -0.5073135

$b
[1] 6.54052

Running 2, completed 1/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] 1.362881

$b
[1] 3.985368

Running 3, completed 2/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] -0.7663256

$b
[1] -0.7330135

Running 4, completed 3/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] 1.039193

$b
[1] 0.4264163

Running 5, completed 4/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] 0.6365823

$b
[1] -5.741255

Running 6, completed 5/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] 0.02302522

$b
[1] -9.043764

Running 7, completed 6/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] 1.643261

$b
[1] -6.151851

Running 8, completed 7/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] 0.38148

$b
[1] 9.197522

Running 9, completed 8/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] 1.896417

$b
[1] 5.952341

Running 10, completed 9/10 Wed Aug 04 9:06:01 PM 2021
$a
[1] -0.2940408

$b
[1] -2.536415

> h1$add_EI(n = 1)
> h1$run_all()
Running 11, completed 10/11 Wed Aug 04 9:06:02 PM 2021
$a
[1] -0.04135399

$b
[1] 0.2916269

> #system.time(h1$run_EI_for_time(sec=3, batch_size = 1))
> #system.time(h1$run_EI_for_time(sec=3, batch_size = 3))
> h1$plotorder()
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Namespaces in Imports field not imported from:
  'PearsonDS' 'VGAM' 'actuar' 'fExtremes' 'rmutil'
  All declared Imports should be used.
Packages required but not available: 'comperes', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spdep', 'Hmisc', 'nonparaeff'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'patchwork'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Directional', 'pchc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'otsad', 'tsoutliers', 'forecast', 'anomalize', 'dplyr', 'tibble',
  'ggplot2', 'tidyr', 'kableExtra'

Packages suggested but not available for checking: 'tourr', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'janitor', 'readr', 'rvest', 'sf', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr'
Error(s) in re-building vignettes:
--- re-building 'comtradr-vignette.Rmd' using rmarkdown
Quitting from lines 232-249 (comtradr-vignette.Rmd) 
Error: processing vignette 'comtradr-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'comtradr-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running examples in 'con2lki-Ex.R' failed
The error most likely occurred in:

> ### Name: con2lki
> ### Title: Calculate lki from contaminants
> ### Aliases: con2lki
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Packages required but not available: 'sf', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'survminer', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'bench', 'rms', 'brms', 'rstan', 'rstanarm',
  'bayesplot', 'vdiffr', 'ggtext', 'patchwork', 'cowplot', 'reprex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'roxygen2', 'sessioninfo', 'testthat'
Running 'spelling.R'
  Running 'tests.R'
Running the tests in 'tests/tests.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
Quitting from lines 196-206 (README.Rmd) 
Error: processing vignette 'README.Rmd' failed with diagnostics:
there is no package called 'sessioninfo'
--- failed re-building 'README.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'bigrquery'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'hdrcde', 'parsnip', 'mlr', 'caret', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'hdrcde', 'testthat'
Packages suggested but not available for checking:
  'dplyr', 'pkgdown', 'testthat'
Namespace in Imports field not imported from: 'memoise'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (C) 2019 LINE Corporation
  > #
  > # conflr is free software; you can redistribute it and/or modify it under the
  > # terms of the GNU General Public License as published by the Free Software
  > # Foundation, version 3.
  > #
  > # conflr is distributed in the hope that it will be useful, but WITHOUT ANY
  > # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
  > # A PARTICULAR PURPOSE. See <http://www.gnu.org/licenses/> for more details.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'caret', 'ggplot2', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'usethis'
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'dplyr', 'miceadds'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'ggplot2', 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dbplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: 'lintr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'dendextend', 'dplyr', 'ggplot2', 'ggrepel', 'leidenAlg',
  'sccore'

Packages suggested but not available for checking:
  'BiocParallel', 'conosPanel', 'DESeq2', 'ggrastr', 'p2data',
  'pagoda2', 'rhdf5', 'Seurat', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'tibble', 'rnaturalearth', 'sf'

Packages suggested but not available for checking: 'testthat', 'alphahull'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'GGally', 'ggplot2', 'ggrepel', 'network', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'janitor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'GA', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'devtools', 'testthat'
Packages suggested but not available for checking: 'testthat', 'vroom'
Packages suggested but not available for checking:
  'testthat', 'devtools', 'ggplot2', 'vdiffr'
Running examples in 'contoureR-Ex.R' failed
The error most likely occurred in:

> ### Name: contourLinesR
> ### Title: Get Contour Lines (list)
> ### Aliases: contourLinesR
> 
> ### ** Examples
> 
> library(contoureR)
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running examples in 'ContourFunctions-Ex.R' failed
The error most likely occurred in:

> ### Name: gcf
> ### Title: Make contour plot from data or function using ggplot2
> ### Aliases: gcf
> 
> ### ** Examples
> 
> gcf(function(x){x[1]^2 - x[2]})
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: gcf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_the_cf_R_package.Rmd' using rmarkdown
Quitting from lines 171-173 (Introduction_to_the_cf_R_package.Rmd) 
Error: processing vignette 'Introduction_to_the_cf_R_package.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Introduction_to_the_cf_R_package.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'rms'

Packages suggested but not available for checking:
  'kableExtra', 'dplyr', 'ggplot2', 'tidyr', 'testthat', 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr', 'gh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'SHELF'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'eurostat', 'tidyr', 'broom', 'ggpubr'

Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'readr', 'readxl', 'tidyverse', 'rvest',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'srvyr'
Packages required but not available: 'fields', 'StatMatch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ClustGeo'

Package suggested but not available for checking: 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rgbif', 'rnaturalearth'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'fitbitViz', 'tmap', 'leaflet', 'leafgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'flexsurv', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'ggplot2'

Package suggested but not available for checking: 'bayesplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'BiocParallel'
Namespace in Imports field not imported from: 'mcc'
  All declared Imports should be used.
Packages suggested but not available for checking: 'testthat', 'StatMatch'
Running 'test.R'
Running the tests in 'tests/test.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: 'ExplainPrediction'
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'car', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'detectseparation', 'phyloseq'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'roxygen2', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'fitFunction.Rmd' using rmarkdown
Quitting from lines 17-22 (fitFunction.Rmd) 
Error: processing vignette 'fitFunction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'fitFunction.Rmd'

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

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'gganimate', 'ggplot2', 'qicharts2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Packages suggested but not available for checking:
  'dplyr', 'plotly', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'padr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'shinytest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'

Package which this enhances but not available for checking: 'quanteda'
Packages required but not available: 'quanteda', 'RNewsflow'

Packages suggested but not available for checking: 'testthat', 'gender'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'xcms'
Packages required but not available:
  'ggplot2', 'recipes', 'plotly', 'tibble', 'dplyr', 'tidyr',
  'ggrepel', 'forcats', 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggcorrplot', 'ggplot2', 'gt', 'Hmisc',
  'rstanarm', 'see', 'testthat', 'tidyr'
Running examples in 'correlation-Ex.R' failed
The error most likely occurred in:

> ### Name: simulate_simpson
> ### Title: Simpson's paradox dataset simulation
> ### Aliases: simulate_simpson
> 
> ### ** Examples
> 
> data <- simulate_simpson(n = 100, groups = 5, r = 0.5)
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages required but not available: 'ingredients', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'DALEX'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tibble', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'dbplyr', 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'forecast', 'hts', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # file corset/tests/testthat.R
  > # Copyright (C) 2016 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co.
  > # , Inc., Kenilworth, NJ, USA.
  > #
  > # This program is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with this program.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggcorrplot', 'ggpubr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cosinor', 'cowplot', 'ggplot2', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'cowplot', 'ggquiver'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'OpenMx', 'ctsem', 'MBESS', 'scholar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'colordistance'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'flexsurv', 'car', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ## Test `countrycode` using the `testthat` package
  > 
  > ## Setup
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dataRetrieval', 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'hurricaneexposure'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'choroplethr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'gstat'
  All declared Imports should be used.
Package suggested but not available for checking: 'qgraph'
Error(s) in re-building vignettes:
--- re-building 'CovCombR.rmd' using rmarkdown
Quitting from lines 66-68 (CovCombR.rmd) 
Error: processing vignette 'CovCombR.rmd' failed with diagnostics:
there is no package called 'qgraph'
--- failed re-building 'CovCombR.rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'colourpicker', 'dplyr', 'egg', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'mrgsolve', 'ggridges', 'ggrepel', 'ggstance', 'patchwork', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'plotly', 'dplyr'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rio', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'EpiEstim', 'cli', 'dplyr', 'gt', 'tibble', 'tidyr', 'janitor',
  'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Packages suggested but not available for checking: 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'readr', 'rvest', 'pointblank'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: 'wbstats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'dplyr', 'mapview', 'plotly', 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'sf', 'tidyr'

Packages suggested but not available for checking:
  'httptest', 'mockery', 'testthat', 'tibble', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'dplyr', 'projmgr', 'readxl', 'tibble'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'ggpubr', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readxl', 'tibble', 'tidyr', 'vroom'

Packages suggested but not available for checking:
  'ggplot2', 'ggspatial', 'mockery', 'pkgdown', 'rvest', 'rworldmap',
  'sf', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'usethis'
Package required but not available: 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'mockery'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ops <- options("crayon.enabled" = FALSE, warn = 1)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespaces in Imports field not imported from:
  'Rcpp' 'gsl'
  All declared Imports should be used.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'patchwork', 'testthat', 'tidyr', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'multicolor', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'cowsay_tutorial.Rmd' using rmarkdown
Quitting from lines 111-113 (cowsay_tutorial.Rmd) 
Error: processing vignette 'cowsay_tutorial.Rmd' failed with diagnostics:
there is no package called 'multicolor'
--- failed re-building 'cowsay_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'rms', 'dplyr', 'tidyr', 'ggplot2', 'mediation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MESS', 'qvalue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat'
Namespaces in Imports field not imported from:
  'Rdpack' 'grDevices'
  All declared Imports should be used.
Package suggested but not available for checking: 'qvalue'
Packages suggested but not available for checking:
  'bench', 'cli', 'decor', 'ggplot2', 'mockery', 'testthat', 'tibble'
Running examples in 'cpp11-Ex.R' failed
The error most likely occurred in:

> ### Name: cpp_register
> ### Title: Generates wrappers for registered C++ functions
> ### Aliases: cpp_register
> 
> ### ** Examples
> 
> # create a minimal package
> dir <- tempfile()
> dir.create(dir)
> 
> writeLines("Package: testPkg", file.path(dir, "DESCRIPTION"))
> writeLines("useDynLib(testPkg, .registration = TRUE)", file.path(dir, "NAMESPACE"))
> 
> # create a C++ file with a decorated function
> dir.create(file.path(dir, "src"))
> writeLines("[[cpp11::register]] int one() { return 1; }", file.path(dir, "src", "one.cpp"))
> 
> # register the functions in the package
> cpp_register(dir)
Error: The cli, decor, tibble package(s) are required for this functionality
Execution halted
Package required but not available: 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'geepack', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr', 'forcats'

Packages suggested but not available for checking: 'srvyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'NMF'
Packages required but not available: 'dplyr', 'rmapshaper', 'sf', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(crayon)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: 'memisc'
Packages required but not available: 'ggplot2', 'ggpubr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'cli'

Package suggested but not available for checking: 'pdp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggstance'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'UpSetR', 'ggplot2', 'ggridges'

Packages suggested but not available for checking:
  'testthat', 'readxl', 'clusterProfiler'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tibble', 'dplyr', 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'gt', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rtracklayer'

Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'DiagrammeR', 'testthat'
Namespaces in Imports field not imported from:
  'R6' 'igraph'
  All declared Imports should be used.
Packages required but not available: 'DiagrammeR', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'ggmcmc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'purrrlyr'

Packages suggested but not available for checking: 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nbpMatching'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'forcats', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'gt', 'ggplot2', 'Hmisc', 'sloop', 'testthat', 'waldo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'openVA'
Error(s) in re-building vignettes:
--- re-building 'using-crossva-and-openva.Rmd' using rmarkdown
Quitting from lines 14-17 (using-crossva-and-openva.Rmd) 
Error: processing vignette 'using-crossva-and-openva.Rmd' failed with diagnostics:
there is no package called 'openVA'
--- failed re-building 'using-crossva-and-openva.Rmd'

SUMMARY: processing the following file failed:
  'using-crossva-and-openva.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'haven', 'labelled', 'readr', 'readxl', 'tibble'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'httptest', 'tibble'

Packages suggested but not available for checking: 'vdiffr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readr', 'tidytext', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'dplyr', 'mapview'

Packages suggested but not available for checking:
  'mapboxapi', 'tigris', 'tidycensus', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

Packages suggested but not available for checking: 'testthat', 'adabag'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'haven', 'httptest', 'lintr', 'styler', 'testthat'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Packages suggested but not available for checking:
  'httptest', 'shinytest', 'testthat'
Packages required but not available: 'dplyr', 'marmap', 'swfscDAS'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr', 'cli'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'MTZ.Rmd' using rmarkdown
--- finished re-building 'MTZ.Rmd'

--- re-building 'SHELX.Rmd' using rmarkdown
Quitting from lines 48-54 (SHELX.Rmd) 
Error: processing vignette 'SHELX.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'SHELX.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'BMisc', 'qte'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rms', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'exactci'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cli'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'plotly', 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

Package suggested but not available for checking: 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fuzzyjoin', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'rmapshaper'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 's2dv'

Packages suggested but not available for checking: 'testthat', 'CSTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sf'

Package suggested but not available for checking: 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'ggplot2', 'haven'

Packages suggested but not available for checking: 'testthat', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  's2dverification', 's2dv', 'ggplot2', 'verification'

Packages suggested but not available for checking: 'testthat', 'startR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'epitools' 'rpivotTable' 'shinyMatrix'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'CTD_Lab-Exercise.Rmd' using rmarkdown
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Quitting from lines 414-507 (CTD_Lab-Exercise.Rmd) 
Error: processing vignette 'CTD_Lab-Exercise.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building 'CTD_Lab-Exercise.Rmd'

SUMMARY: processing the following file failed:
  'CTD_Lab-Exercise.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'markovchain'
Running examples in 'ctmcd-Ex.R' failed
The error most likely occurred in:

> ### Name: expmMC
> ### Title: Matrix Exponential Function
> ### Aliases: expmMC
> 
> ### ** Examples
> 
> ### Exemplary Transition Matrix
> tm0=matrix(1:16,4,4)
> tm0=tm0/rowSums(tm0)
> tm0[4,]=c(0,0,0,1)
> 
> ### Generator Matrix Estimate
> gm_est=gm(tm0,te=1,method="DA")
> gm_est
Call:
gm.default(tm = tm0, te = 1, method = "DA")

Parameters:
       [,1]   [,2]   [,3]   [,4]
[1,] -13.18  12.47   0.00 0.7098
[2,]  10.51 -25.61  14.51 0.5954
[3,]   0.00  12.54 -13.04 0.5064
[4,]   0.00   0.00   0.00 0.0000
> 
> ### Matrix Exponential and Conversion to markovchain object 
> ### (markovchain package needs to be installed)
> mc=expmMC(gm_est,.5)
Error: markovchain is needed for this function to work. Please install it.
Execution halted
Package required but not available: 'fda'

Package suggested but not available for checking: 'crawl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 36-71 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'parsedate', 'sf'
Package unavailable to check Rd xrefs: 'parsedate'
Packages required but not available: 'dplyr', 'Gmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pch'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvest'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ctsem', 'OpenMx'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'pkgbuild', 'rstan', 'RcppParallel', 'tibble',
  'StanHeaders'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'pillar', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dplyr', 'tidyrules'
Package unavailable to check Rd xrefs: 'caret'
Error(s) in re-building vignettes:
--- re-building 'cubist.Rmd' using rmarkdown
Quitting from lines 12-18 (cubist.Rmd) 
Error: processing vignette 'cubist.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'cubist.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'lmerTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Running 'engine.R'
  Comparing 'engine.Rout' to 'engine.Rout.save' ...4d3
< Using libcurl 7.64.1 with Schannel
  Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'hdrcde'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'recipes', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'

Package which this enhances but not available for checking: 'vdiffr'
Error(s) in re-building vignettes:
--- re-building 'cusum.Rmd' using rmarkdown
--- finished re-building 'cusum.Rmd'

--- re-building 'gscusum.Rmd' using rmarkdown
Quitting from lines 13-22 (gscusum.Rmd) 
Error: processing vignette 'gscusum.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'gscusum.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'set', 'do'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'ggplot2', 'ggpubr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'MBESS'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tableone'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggrepel'
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Loading required package: MASS
Loading required package: limSolve
Quitting from lines 26-29 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'dplyr', 'tidyr', 'ggbeeswarm'
Error(s) in re-building vignettes:
--- re-building 'how_to_test_CVs.Rmd' using rmarkdown
Quitting from lines 108-116 (how_to_test_CVs.Rmd) 
Error: processing vignette 'how_to_test_CVs.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'how_to_test_CVs.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'geepack', 'pkgdown'
Running examples in 'cvGEE-Ex.R' failed
The error most likely occurred in:

> ### Name: cv_gee
> ### Title: Proper Scoring Rules for Generalized Estimating Equations
> ### Aliases: cv_gee
> 
> ### ** Examples
> 
> library("geepack")
Error in library("geepack") : there is no package called 'geepack'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Scoring_Rules_GEE.Rmd' using rmarkdown
Quitting from lines 15-23 (Scoring_Rules_GEE.Rmd) 
Error: processing vignette 'Scoring_Rules_GEE.Rmd' failed with diagnostics:
there is no package called 'geepack'
--- failed re-building 'Scoring_Rules_GEE.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rearrr', 'recipes', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggimage', 'ggnewscale', 'groupdata2', 'testthat', 'xpectr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'computeError.Rmd' using rmarkdown
Loading required package: Matrix
Loaded glmnet 4.1-2

Attaching package: 'cvwrapr'

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

    coxnet.deviance

--- finished re-building 'computeError.Rmd'

--- re-building 'kfoldcv.Rmd' using rmarkdown
Quitting from lines 59-63 (kfoldcv.Rmd) 
Error: processing vignette 'kfoldcv.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'kfoldcv.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'testthat'

Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
Running 'group00.R'
Running the tests in 'tests/group00.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'cli'

Packages suggested but not available for checking: 'tidytext', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'dplyr', 'testthat', 'hydroPSO'
Package suggested but not available for checking: 'leaflet'
Error(s) in re-building vignettes:
--- re-building 'cycling_data_analysis.Rmd' using rmarkdown
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building 'cycling_data_analysis.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'sf'

Package suggested but not available for checking: 'stplanr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flexsurv'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Andromeda', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'shinyFiles'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'cowplot'

Package suggested but not available for checking: 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'tibble', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'devtools', 'dplyr', 'ggplot2', 'ggrepel', 'questionr',
  'recipes'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'titanic'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

Package which this enhances but not available for checking: 'treemap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'forcats', 'ggforce', 'ggbeeswarm',
  'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RMariaDB', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gargle', 'googleCloudStorageR'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'ggtree', 'tidytree', 'tidyr',
  'tibble'

Package which this enhances but not available for checking: 'doMC'
Running examples in 'DAISIE-Ex.R' failed
The error most likely occurred in:

> ### Name: are_max_rates_gt_rates
> ### Title: Check if maximum rates are greater or equal to rates
> ### Aliases: are_max_rates_gt_rates
> ### Keywords: internal
> 
> ### ** Examples
> 
> rates <- list(
+   ext_rate = 0.1,
+   immig_rate = 0.1,
+   ana_rate = 0.1,
+   clado_rate = 0.1
+ )
> max_rates <- list(
+   ext_max_rate = 1,
+   immig_max_rate = 1,
+   ana_max_rate = 1,
+   clado_max_rate = 1
+ )
> testthat::expect_true(
+   DAISIE:::are_max_rates_gt_rates(
+     rates = rates,
+     max_rates = max_rates
+   )
+ )
Error in loadNamespace(x) : there is no package called 'testthat'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv(R_TESTS = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'iBreakDown', 'ingredients'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DALEX', 'ggplot2'

Packages suggested but not available for checking:
  'auditor', 'ingredients', 'ggrepel', 'iml', 'lime', 'localModel',
  'mlr', 'recipes', 'testthat', 'tidymodels'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'rstan', 'ggplot2', 'haven', 'janitor', 'tidyr', 'tibble',
  'dplyr', 'jtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'lintr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'testthat', 'ggetho', 'zeitgebr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'janitor', 'readxl'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rtweet'
Packages required but not available: 'tibble', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'xesreadR', 'bupaR', 'readr', 'edeaR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adegenet', 'klaR', 'plotly'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'tidyr', 'StAMPP', 'PopGenReport',
  'hierfstat', 'HardyWeinberg', 'dplyr', 'devtools'

Packages suggested but not available for checking:
  'pegas', 'leaflet.minicharts', 'leaflet', 'poppr', 'qvalue', 'vcfR',
  'mmod', 'plotly', 'ggthemes', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Resolves environment issues when running devtools::check()
  > Sys.setenv(R_TESTS = "")
  > 
  > testthat::test_check(package = "dashboardthemes")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages suggested but not available for checking: 'dash', 'plotly'
Package suggested but not available for checking: 'dash'
Packages suggested but not available for checking:
  'testthat', 'DBItest', 'Andromeda', 'dplyr'
Package unavailable to check Rd xrefs: 'Andromeda'
Package required but not available: 'GeneralizedUmatrix'

Packages suggested but not available for checking:
  'DataVisualizations', 'spdep', 'AdaptGauss',
  'ProjectionBasedClustering', 'parallelDist', 'dendextend'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'summarytools', 'dplyr', 'plotly', 'shinyFiles'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'haven', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'nycflights13'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'GA'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readxl'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'haven'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'rio', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'datapack', 'parsedate'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'devtools', 'httptest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'roxygen2', 'devtools', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'redland'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Packages suggested but not available for checking: 'tibble', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'kableExtra', 'testthat'
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'ggpubr'

Packages suggested but not available for checking:
  'patchwork', 'testthat', 'tibble', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'dataresqc-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_decimals
> ### Title: Plot decimals
> ### Aliases: plot_decimals
> 
> ### ** Examples
> 
> plot_decimals(Rosario$Tx, outfile = paste0(tempdir(),"/test.pdf"))
Error: Package "ggplot2" needed for this function to work. Please install it.
Execution halted
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'lintr', 'stubthat', 'doBy', 'ggplot2'
Packages required but not available:
  'EML', 'readr', 'tibble', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'styler', 'lintr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # datastructures: Implementation of core datastructures for R.
  > #
  > # Copyright (C) Simon Dirmeier
  > #
  > # This file is part of datastructures.
  > #
  > # datastructures is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # datastructures is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with datastructures. If not, see <http://www.gnu.org/licenses/>.
  > 
  > 
  > library(datastructures)
  Loading required package: Rcpp
  
  Attaching package: 'datastructures'
  
  The following object is masked from 'package:utils':
  
      stack
  
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'treemap', 'DiagrammeR', 'mockery'
Package unavailable to check Rd xrefs: 'DiagrammeR'
Running examples in 'data.tree-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in plot.Node(acme) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Error(s) in re-building vignettes:
--- re-building 'applications.Rmd' using rmarkdown
Quitting from lines 57-64 (applications.Rmd) 
Error: processing vignette 'applications.Rmd' failed with diagnostics:
there is no package called 'treemap'
--- failed re-building 'applications.Rmd'

--- re-building 'data.tree.Rmd' using rmarkdown
Quitting from lines 121-124 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'treemap'
--- failed re-building 'data.tree.Rmd'

SUMMARY: processing the following files failed:
  'applications.Rmd' 'data.tree.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'assertr', 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'haven', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'ggmap', 'rworldmap', 'choroplethr', 'dplyr', 'parallelDist',
  'ggExtra', 'plotly', 'DatabionicSwarm', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'rstanarm', 'see', 'sjstats', 'testthat'
Package suggested but not available for checking: 'SASxport'
Packages required but not available:
  'babynames', 'dplyr', 'forcats', 'gapminder', 'ggplot2', 'Lahman',
  'nycflights13', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'dplyr', 'forcats', 'ggplot2', 'ggridges', 'readxl',
  'testthat'
Running 'create_testing_df.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'data_preparation.Rmd' using rmarkdown
Quitting from lines 24-32 (data_preparation.Rmd) 
Error: processing vignette 'data_preparation.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'data_preparation.Rmd'

--- re-building 'how-to.Rmd' using rmarkdown
Quitting from lines 12-29 (how-to.Rmd) 
Error: processing vignette 'how-to.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'how-to.Rmd'

SUMMARY: processing the following files failed:
  'data_preparation.Rmd' 'how-to.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'aoos'

Packages suggested but not available for checking:
  'dplyr', 'lintr', 'nycflights13', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TSdist', 'parallelDist', 'caret', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidypredict', 'tidyverse', 'dbplyr', 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'bigrquery', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'RMariaDB', 'testthat'
Package required but not available: 'testthat'

Packages suggested but not available for checking:
  'dblog', 'devtools', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'softImpute'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'RcppParallel', 'tibble'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bnviewer', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'RMariaDB', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'dbplyr', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'Lahman', 'nycflights13', 'RMariaDB', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'dendextend'
Namespace in Imports field not imported from: 'html5'
  All declared Imports should be used.
Packages suggested but not available for checking: 'testthat', 'RMariaDB'
Package suggested but not available for checking: 'Ecdat'
Package unavailable to check Rd xrefs: 'Ecdat'
Running examples in 'DCchoice-Ex.R' failed
The error most likely occurred in:

> ### Name: dbchoice
> ### Title: Parametric approach to analyze double-bounded dichotomous choice
> ###   contingent valuation data
> ### Aliases: dbchoice print.dbchoice vcov.dbchoice logLik.dbchoice
> ### Keywords: DCchoice double-bounded nonlinear
> 
> ### ** Examples
> 
> ## Examples are based on a data set NaturalPark in the package 
> ## Ecdat (Croissant 2011): DBDCCV style question for measuring 
> ## willingness to pay for the preservation of the Alentejo Natural 
> ## Park. The data set (dataframe) contains seven variables: 
> ## bid1 (bid in the initial question), bidh (higher bid in the follow-up 
> ## question), bidl (lower bid in the follow-up question), answers 
> ## (response outcomes in a factor format with four levels of "nn", 
> ## "ny", "yn", "yy"), respondents' characteristic variables such 
> ## as age, sex and income (see NaturalPark for details).
> data(NaturalPark, package = "Ecdat")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'Ecdat'
Calls: data -> find.package
Execution halted
Packages required but not available: 'rumidas', 'roll'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'golem', 'readr', 'readxl', 'skimr', 'tibble', 'visdat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'WGCNA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'idefix', 'mlogit', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dnet'

Package suggested but not available for checking: 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BiocParallel', 'dplyr', 'tidyr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rstan'

Package suggested but not available for checking: 'BRugs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DCluster'

Package suggested but not available for checking: 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'CDM'
  All declared Imports should be used.
Package required but not available: 'dclone'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'dplyr', 'forcats', 'janitor', 'tibble',
  'tidyr', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'gtsummary', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'fda.usc'
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.unsetenv("R_TESTS")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble'
Running examples in 'ddi-Ex.R' failed
The error most likely occurred in:

> ### Name: ddc
> ### Title: Data Defect Correlation
> ### Aliases: ddc
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called 'tibble'
Execution halted
Packages suggested but not available for checking: 'testthat', 'tidyr'
Namespaces in Imports field not imported from:
  'MASS' 'qpdf'
  All declared Imports should be used.
Packages required but not available: 'readr', 'haven', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tibble'

Packages suggested but not available for checking: 'ggExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggalt', 'MEGENA', 'Hmisc'

Packages suggested but not available for checking: 'WGCNA', 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'plotly', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'chillR', 'dplyr', 'ggplot2', 'ggstance', 'patchwork', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'AER', 'dplyr', 'tibble', 'ggplot2', 'broom', 'sf'
Error(s) in re-building vignettes:
--- re-building 'decoder.Rmd' using rmarkdown
--- finished re-building 'decoder.Rmd'

--- re-building 'sjukhus.Rmd' using rmarkdown
Quitting from lines 54-70 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'sjukhus.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'PSF', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'usethis', 'StratigrapheR', 'hht', 'dplyr'

Packages suggested but not available for checking:
  'EMD', 'Rssa', 'astrochron', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19'

Package suggested but not available for checking: 'VariantAnnotation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'cowplot', 'ggplot2'
Package required but not available: 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Deducer', 'klaR'

Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'car'

Package suggested but not available for checking: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Deducer', 'OpenStreetMap', 'Hmisc'

Depends: includes the non-default packages:
  'JavaGD', 'Deducer', 'sp', 'maptools', 'OpenStreetMap', 'scales',
  'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'usage-and-algorithm-explained.Rmd' using rmarkdown
Quitting from lines 19-23 (usage-and-algorithm-explained.Rmd) 
Error: processing vignette 'usage-and-algorithm-explained.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'usage-and-algorithm-explained.Rmd'

SUMMARY: processing the following file failed:
  'usage-and-algorithm-explained.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'caret'
Packages required but not available: 'ggforce', 'ggplot2', 'ggraph'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fastDummies'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'ggthemes'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggnewscale'

Packages suggested but not available for checking:
  'tidyverse', 'ggforce', 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'SASxport'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gptk'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'DiagrammeR', 'roxygen2', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #R
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'assertthat'
  All declared Imports should be used.
Packages required but not available:
  'rstan', 'rstantools', 'dplyr', 'ggplot2', 'broom', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Bchron'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'ftsa', 'rainbow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'ClusterR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'viridis'

Packages suggested but not available for checking: 'testthat', 'heatmaply'

Packages which this enhances but not available for checking:
  'ggdendro', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > # Run all tests for gphys package
  > #  
  > # Author: jefferis
  > ###############################################################################
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'oce', 'dplyr', 'plotly', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gapmap'
Packages required but not available: 'ggplot2', 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FactoMineR'

Package suggested but not available for checking: 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
Packages required but not available: 'rstan', 'RcppParallel', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'usethis', 'devtools', 'roxygen2', 'ggplot2', 'cowplot'
Running examples in 'denvax-Ex.R' failed
The error most likely occurred in:

> ### Name: lazou2016
> ### Title: The serosurvey data in L'Azou 2016
> ### Aliases: lazou2016
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(denvax); require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
> data(lazou2016)
> ggplot(lazou2016) + aes(Age, Seropositive/Number*100, color = Country) +
+   geom_point() + labs(y="Seropositive %", x="Age Group") + lims(y=c(0,100)) +
+   theme_minimal()
Error in ggplot(lazou2016) : could not find function "ggplot"
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'Hmisc', 'rms', 'tibble', 'tidyr', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'fda', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr'

VignetteBuilder packages required for checking but not installed:
  'ggplot2', 'dplyr', 'tidyr'
Errors in running code in vignettes:
when running code in 'derivmkts-vignette.Rmd'
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'ggplot2' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'derivmkts-vignette.Rmd' using 'UTF-8'... failed to complete the test
Packages suggested but not available for checking: 'testthat', 'gh'
Packages required but not available:
  'dplyr', 'forcats', 'tibble', 'tidyr', 'broom', 'haven', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'GGally'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'lintr'
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'exact2x2', 'dplyr', 'tibble', 'forcats', 'cli', 'kableExtra'

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'forcats', 'cli'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'datasets'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'Hmisc', 'caret', 'car', 'forecast', 'UsingR', 'memisc'
Packages required but not available: 'fields', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'lmerTest', 'afex', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sessioninfo', 'testthat', 'tibble'
Error(s) in re-building vignettes:
--- re-building 'custom.Rmd' using rmarkdown
--- finished re-building 'custom.Rmd'

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

--- re-building 'engine.Rmd' using rmarkdown
Warning: The internal function knitr:::wrap.knit_image_paths has been deprecated. Please use knitr::sew() on an object of the class 'knit_image_paths' instead.
--- finished re-building 'engine.Rmd'

--- re-building 'objects.Rmd' using rmarkdown
Quitting from lines 38-41 (objects.Rmd) 
Error: processing vignette 'objects.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'objects.Rmd'

--- re-building 'sessioninfo.Rmd' using rmarkdown
Quitting from lines 26-33 (sessioninfo.Rmd) 
Error: processing vignette 'sessioninfo.Rmd' failed with diagnostics:
there is no package called 'sessioninfo'
--- failed re-building 'sessioninfo.Rmd'

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

SUMMARY: processing the following files failed:
  'objects.Rmd' 'sessioninfo.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'dclone', 'dcmle'
Package required but not available: 'pkgload'

Packages suggested but not available for checking: 'testthat', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'autothresholdr', 'dplyr', 'ijtiff', 'RcppParallel'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RColorBrewer'
  All declared Imports should be used.
Packages required but not available:
  'usethis', 'cli', 'pkgbuild', 'pkgload', 'rcmdcheck', 'roxygen2',
  'sessioninfo', 'testthat'

Packages suggested but not available for checking:
  'foghorn', 'gh', 'gmailr', 'lintr', 'mockery', 'pkgdown', 'rhub'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Quitting from lines 38-42 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'my-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dexter', 'shinyFiles', 'dplyr', 'tidyr', 'tibble', 'readxl',
  'readODS', 'ggplot2', 'ggExtra', 'ggridges'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dexter', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MVN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'AER', 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggpubr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'ggplot2', 'plotly'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MLInterfaces'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'WGCNA'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'MEGENA', 'doMC', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'biomaRt'
Packages required but not available:
  'dplyr', 'tidyr', 'qvalue', 'sva', 'zFPKM'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'phyr'
Packages required but not available: 'forecast', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'haven', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'tibble', 'tidyr', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggvoronoi', 'sf', 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'pillar', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'dialr.Rmd' using rmarkdown
Quitting from lines 18-21 (dialr.Rmd) 
Error: processing vignette 'dialr.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'dialr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tibble', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'klaR', 'NMF', 'tidyr', 'yardstick'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'dplyr'

Packages suggested but not available for checking: 'haven', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BMisc', 'ggplot2', 'ggpubr', 'DRDID'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'dielectric-Ex.R' failed
The error most likely occurred in:

> ### Name: AgPalik
> ### Title: AgPalik
> ### Aliases: AgPalik
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgPalik)
> str(AgPalik$raw())
'data.frame':	241 obs. of  4 variables:
 $ wavelength: num  0.155 0.207 0.248 0.275 0.31 ...
 $ epsilon   : cplx  1+0i 1+0i 1+0i ...
 $ real      : num  1 1 1 1 1.01 ...
 $ imag      : num  5.84e-06 1.68e-05 3.04e-05 4.42e-05 7.16e-05 ...
> AgPalik$comment
$source
[1] "Silver in the visible, Palik"

$units
[1] "nanometres"

> demo(AgPalik)


	demo(AgPalik)
	---- ~~~~~~~

> library(dielectric)

> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Calls: demo -> source -> withVisible -> eval -> eval -> library
Execution halted
Package required but not available: 'rfishbase'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'ggnewscale'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyverse', 'sf', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'randomNames', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'bernstein.Rnw' using knitr
Sampling sensitivity with m=500 gamma=0.2 k=439
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'bernstein.Rnw'

--- re-building 'diffpriv.Rnw' using knitr
Quitting from lines 296-310 (diffpriv.Rnw) 
Error: processing vignette 'diffpriv.Rnw' failed with diagnostics:
there is no package called 'randomNames'
--- failed re-building 'diffpriv.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # diffusr: network diffusion algorithms in R
  > #
  > # Copyright (C) 2016 Simon Dirmeier
  > #
  > # This file is part of diffusr.
  > #
  > # diffusr is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # diffusr is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with diffusr. If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'ShinyItemAnalysis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TestDataImputation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  digest.c:207:25: warning: too many arguments for format [-Wformat-extra-args]
  digest.c:432:25: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/digest/digest.Rcheck/00install.out' for details.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'FactoMineR', 'ggrepel', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'NMF', 'ggplot2', 'testthat', 'tidyr'
Package unavailable to check Rd xrefs: 'NMF'
Running examples in 'dimRed-Ex.R' failed
The error most likely occurred in:

> ### Name: NNMF-class
> ### Title: Non-Negative Matrix Factorization
> ### Aliases: NNMF-class NNMF
> 
> ### ** Examples
> 
> dat <- loadDataSet("Iris")
> 
> set.seed(4646)
> factorization <- embed(dat, "NNMF")
Error in chckpkg("NMF") : 
  require 'NMF' package, install it using install.packages('NMF')
Calls: embed ... embed -> .local -> do.call -> <Anonymous> -> chckpkg
Execution halted
Error(s) in re-building vignettes:
--- re-building 'dint.Rmd' using rmarkdown
Quitting from lines 244-245 (dint.Rmd) 
Error: processing vignette 'dint.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'dint.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'WGCNA', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'usethis', 'ggplot2', 'lemon', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RcppParallel', 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'sandwich'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'DirectEffects.Rmd' using rmarkdown
Quitting from lines 14-20 (DirectEffects.Rmd) 
Error: processing vignette 'DirectEffects.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'DirectEffects.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'bigstatsr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'alphahull', 'dplyr', 'ggthemes', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'examples.Rmd' using knitr
Quitting from lines 16-76 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'examples.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'haven'

Packages suggested but not available for checking: 'testthat', 'EdSurvey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'cowplot'

Packages suggested but not available for checking:
  'testthat', 'INLA', 'SpatialEpi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'shinytest', 'testthat', 'vdiffr'
Packages required but not available: 'TSCAN', 'philentropy', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'ggdendro', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 27-31 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'introduction.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'psych'
  All declared Imports should be used.
Packages required but not available:
  'ggpubr', 'GGally', 'network', 'ggplot2', 'dplyr', 'ggrepel', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'golem', 'plotly', 'ggplot2', 'ggdendro', 'echarts4r', 'colourpicker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'FactoMineR'
Packages required but not available: 'parsnip', 'dials', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'klaR', 'sparsediscrim', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'caret', 'Ecdat', 'pec'
Running examples in 'discSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: adjDevResid
> ### Title: Adjusted Deviance Residuals
> ### Aliases: adjDevResid
> ### Keywords: survival
> 
> ### ** Examples
> 
> # Example with cross validation and unemployment data 
> library(Ecdat)
Error in library(Ecdat) : there is no package called 'Ecdat'
Execution halted
Running 'UnitTestsDiscSurvDataTransform.R'
  Running 'UnitTestsDiscSurvEstimation.R'
  Running 'UnitTestsDiscSurvEvalShort.R'
  Running 'UnitTestsDiscSurvEvaluation.R'
Running the tests in 'tests/UnitTestsDiscSurvEvaluation.R' failed.
Complete output:
  > library(discSurv)
  > library(pec)
  Error in library(pec) : there is no package called 'pec'
  Execution halted
Packages suggested but not available for checking: 'sf', 'mapview'
Running examples in 'disdat-Ex.R' failed
The error most likely occurred in:

> ### Name: AWT
> ### Title: Australian Wet Tropics species distribution data
> ### Aliases: AWT
> ### Keywords: datasets
> 
> ### ** Examples
> 
> awt_po <- disPo("AWT")
> awt_bg <- disBg("AWT")
> 
> awt_pa_plant <- disPa("AWT", "plant")
> awt_env_plant <- disEnv("AWT", "plant")
> awt_pa_bird <- disPa("AWT", "bird")
> awt_env_bird <- disEnv("AWT", "bird")
> 
> 
> # Or all in one list
> awt <- disData("AWT")
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Calls: disData -> do.call -> <Anonymous> -> rbind
Execution halted
Package suggested but not available for checking: 'spdep'

Package which this enhances but not available for checking: 'INLA'
Packages required but not available:
  'dplyr', 'systemfit', 'tibble', 'tidyr', 'RcppParallel'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'benchmarkme'

Packages suggested but not available for checking:
  'testthat', 'nycflights13', 'readr', 'broom', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat', 'tidyr', 'skimr', 'ggplot2',
  'ggridges', 'gghalves', 'bench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'geomorph'
Packages required but not available: 'caret', 'dplyr', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'viridis'

Packages suggested but not available for checking: 'devtools', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'factoextra', 'ggplot2', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'plotly'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'ggdist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'GA', 'AdaptGauss'

Package suggested but not available for checking: 'parallelDist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'testthat'
Packages suggested but not available for checking: 'tidyverse', 'testthat'
Package required but not available: 'testthat'

Packages suggested but not available for checking:
  'dplyr', 'dbplyr', 'nycflights13', 'RMariaDB', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'ggmulti', 'loon.ggplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'entropart'
Packages required but not available: 'ggplot2', 'ggpubr', 'rms'

Packages suggested but not available for checking: 'testthat', 'BOLTSSIRR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'qgraph'

Packages suggested but not available for checking: 'sendplot', 'HWxtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'tibble', 'tidyr', 'ggplot2', 'plotly',
  'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'parsedate'

Packages suggested but not available for checking: 'lintr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nardl', 'dynlm', 'AER', 'roll'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MSEtool', 'dplyr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'geepack'
Packages required but not available:
  'dplyr', 'ggplot2', 'hrbrthemes', 'kableExtra', 'mice', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'forecast', 'nycflights13'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MplusAutomation'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bayesplot', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'EML'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'pillar', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'DiagrammeR', 'nycflights13', 'RMariaDB', 'testthat',
  'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test_vtrack.R'
Running the tests in 'tests/test_vtrack.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readxl', 'tidyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RcppParallel'

Packages suggested but not available for checking: 'testthat', 'testthis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'supraHex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'network', 'ergm', 'sna', 'arm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'OutliersO3', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'dobin.Rmd' using rmarkdown
Quitting from lines 22-34 (dobin.Rmd) 
Error: processing vignette 'dobin.Rmd' failed with diagnostics:
Package OutliersO3 is needed for the vignette. Please install it.
--- failed re-building 'dobin.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'pbkrtest', 'tibble'

Packages suggested but not available for checking: 'geepack', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quanteda', 'textstem'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'roxygen2'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rcmdcheck', 'roxygen2'

Packages suggested but not available for checking:
  'devtools', 'pkgload', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'osmdata', 'RcppParallel'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'roxygen2', 'sf', 'testthat', 'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'agricolae'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'skpr'
Package unavailable to check Rd xrefs: 'skpr'
Packages suggested but not available for checking:
  'testthat', 'car', 'dynlm', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'da-logistic-regression.Rmd' using rmarkdown
Quitting from lines 177-178 (da-logistic-regression.Rmd) 
Error: processing vignette 'da-logistic-regression.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'da-logistic-regression.Rmd'

SUMMARY: processing the following file failed:
  'da-logistic-regression.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'RcmdrMisc'
Packages required but not available: 'dplyr', 'tibble', 'tidytext'

Packages suggested but not available for checking:
  'readr', 'rvest', 'tidyr', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'rvest', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'lmerTest'

Packages suggested but not available for checking: 'devtools', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'doRedis', 'devtools', 'testthat'
Running 'testgFit.R'
  Running 'testplanMod.R'
  Running 'testsDesign.R'
  Running 'testsFitting.R'
  Running 'testsMCPMod.R'
  Running 'testsMCT.R'
  Running 'testsoptContr.R'
  Running 'testsplotDRMod.R'
  Running 'testssampSize.R'
  Running 'testssamplMod.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## Note: Files in this directory are old test cases that accumulated
  > ## historically over time, many of them commented out for time reasons
  > ## (and unorganized due to lack of anything close to testthat at the
  > ## time of creation). The testthat sub-directory now contains a
  > ## selected subset of these tests (with some additions) that have been
  > ## brought in the testthat format.
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'analysis_normal.Rmd' using rmarkdown
Quitting from lines 2-8 (./children/settings.txt) 
Quitting from lines NA-8 (./children/settings.txt) 
Error: processing vignette 'analysis_normal.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'analysis_normal.Rmd'

--- re-building 'binary_data.Rmd' using rmarkdown
Quitting from lines 2-8 (./children/settings.txt) 
Quitting from lines NA-8 (./children/settings.txt) 
Error: processing vignette 'binary_data.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'binary_data.Rmd'

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

--- re-building 'mult_regimen.Rmd' using rmarkdown
Quitting from lines 2-8 (./children/settings.txt) 
Quitting from lines NA-8 (./children/settings.txt) 
Error: processing vignette 'mult_regimen.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'mult_regimen.Rmd'

--- re-building 'overview.Rmd' using rmarkdown
Quitting from lines 2-8 (./children/settings.txt) 
Quitting from lines NA-8 (./children/settings.txt) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'overview.Rmd'

--- re-building 'sample_size.Rmd' using rmarkdown
Quitting from lines 2-8 (./children/settings.txt) 
Quitting from lines NA-8 (./children/settings.txt) 
Error: processing vignette 'sample_size.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'sample_size.Rmd'

SUMMARY: processing the following files failed:
  'analysis_normal.Rmd' 'binary_data.Rmd' 'mult_regimen.Rmd'
  'overview.Rmd' 'sample_size.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'tidyr', 'dplyr', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'case_study.Rmd' using rmarkdown
Quitting from lines 84-99 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'case_study.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 77-80 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following files failed:
  'case_study.Rmd' 'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'rms'
Error(s) in re-building vignettes:
--- re-building 'dosresmeta.Rnw' using knitr
Quitting from lines 330-331 (dosresmeta.Rnw) 
Error: processing vignette 'dosresmeta.Rnw' failed with diagnostics:
there is no package called 'rms'
--- failed re-building 'dosresmeta.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Running 'test_package.R'
Running the tests in 'tests/test_package.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'ggstance'

Packages suggested but not available for checking: 'tibble', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'patrick', 'dplyr', 'AER'
Running 'testthat_regression_tests.R'
Running the tests in 'tests/testthat_regression_tests.R' failed.
Complete output:
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'pkgload'
Packages required but not available: 'readr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'alakazam', 'dplyr', 'ggtree', 'shazam', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CEoptim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exactci', 'ggplot2', 'ggpubr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'forecast', 'testthat'
Packages required but not available: 'tidyverse', 'tidyr'

Package suggested but not available for checking: 'nycflights13'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'pillar'

Packages suggested but not available for checking:
  'bench', 'broom', 'dbplyr', 'Lahman', 'nycflights13', 'testthat',
  'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rio'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'drc', 'devtools', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'golem', 'ggplot2', 'readr', 'dplyr', 'tidyr', 'tibble', 'broom',
  'cowplot', 'ggforce', 'colourpicker', 'rvest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyr', 'tibble', 'dplyr', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'dragracer-intro.Rmd' using rmarkdown
Quitting from lines 18-22 (dragracer-intro.Rmd) 
Error: processing vignette 'dragracer-intro.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'dragracer-intro.Rmd'

SUMMARY: processing the following file failed:
  'dragracer-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'cli', 'disk.frame', 'ggplot2', 'ggraph', 'qs', 'styler', 'testthat',
  'tibble', 'usethis'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("drake_session_info" = "false")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'testthat', 'highcharter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'readxl'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'sde'

Packages suggested but not available for checking:
  'fda', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BMisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fastDummies'

Package suggested but not available for checking: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gapminder', 'gt', 'modelsummary', 'dotwhisker', 'interplot',
  'likert', 'ggthemes', 'summarytools', 'tidyverse', 'car', 'arm',
  'tibble', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DALEX', 'dplyr', 'tidyr', 'ingredients'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyverse', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
Packages required but not available: 'SmartEDA', 'mlr', 'ggplot2', 'iml'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DESeq2', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'ggsci'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'BIGL'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'unikn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'plotly'

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tsoutliers', 'forecast', 'seastests'

Package suggested but not available for checking: 'stR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dssd', 'Distance', 'sf', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tibble', 'tidyr', 'ggplot2', 'dplyr', 'testthat', 'forcats',
  'viridis'
Error(s) in re-building vignettes:
--- re-building 'DSjobtracker.Rmd' using rmarkdown
Quitting from lines 62-63 (DSjobtracker.Rmd) 
Error: processing vignette 'DSjobtracker.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'DSjobtracker.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dsBaseClient', 'mockery', 'testthat', 'tibble'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'Distance', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'opalr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exactci', 'asht'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'ggplot2'

Packages suggested but not available for checking: 'tibble', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'plotly'
Packages required but not available: 'pec', 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'dplyr'

Package suggested but not available for checking: 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'bench', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'RcppParallel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'caret'

Package suggested but not available for checking: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'haven', 'readxl', 'readr', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Seurat'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'DBItest', 'dplyr', 'dbplyr', 'nycflights13', 'testthat'
Packages required but not available:
  'dplyr', 'tidyr', 'tidyverse', 'ggplot2', 'rstatix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'lintr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tsDyn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ncdf4' 'rgdal'
  All declared Imports should be used.
Package required but not available: 'hglasso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Had the same issue as in this thread: https://github.com/hadley/testthat/issues/86
  > # or maybe https://github.com/r-lib/devtools/issues/1526
  > Sys.unsetenv("R_TESTS")
  > 
  > options(deparse.max.lines = 5,  testthat.summary.max_reports = 1000L)
  > testthat::test_check("dynamichazard", reporter = "summary")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'ggplot2', 'viridis', 'ari', 'gganimate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'maptools' 'tools'
  All declared Imports should be used.
Package suggested but not available for checking: 'readxl'
Running examples in 'dynBiplotGUI-Ex.R' failed
The error most likely occurred in:

> ### Name: dynBiplot
> ### Title: Dynamic Biplot
> ### Aliases: dynBiplot
> 
> ### ** Examples
> 
> dynBiplot("en")
Packages required but not available: 'dynutils', 'lmds', 'tibble'

Packages suggested but not available for checking: 'testthat', 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'dynutils', 'dynwrap', 'testthat', 'tidyr', 'tibble'

Package suggested but not available for checking: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'dynutils', 'ggplot2', 'ggraph', 'ggrepel', 'GillespieSSA2',
  'lmds', 'patchwork', 'tibble', 'tidygraph', 'tidyr', 'viridis'

Packages suggested but not available for checking:
  'dynwrap', 'Seurat', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly', 'rms', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dynutils', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'dynutils', 'dynfeature', 'dyndimred', 'dynwrap', 'GA',
  'ggforce', 'ggplot2', 'ggraph', 'ggrepel', 'patchwork', 'tibble',
  'tidyr', 'tidygraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mstate'
Packages required but not available:
  'ggplot2', 'mice', 'fda', 'car', 'tibble'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'DataCombine'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'proxyC', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'babelwhale', 'dplyr', 'dynutils', 'dynparam', 'readr', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'dyndimred', 'pkgload', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TraMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BiocParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DataCombine', 'ggplot2', 'accelerometry'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'eafplot.R'
  Running 'lin-sph.R'
  Running 'ran.100pts.3d.10.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'shinyFiles', 'ggplot2', 'ggthemes', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'leaflet', 'plotly', 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EpiEstim', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'roxygen2', 'incidence', 'projections'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggmap'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'dplyr', 'forcats', 'ggalluvial', 'ggplot2', 'ggridges',
  'recipes', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'nycflights13', 'vdiffr', 'parcats', 'pkgdown',
  'workflows', 'caret', 'parsnip', 'vip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'Hmisc', 'readxl'

Packages suggested but not available for checking: 'qs', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sdcTable'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'verification'
Package unavailable to check Rd xrefs: 'verification'
Packages suggested but not available for checking: 'testthat', 'readxl'

Package which this enhances but not available for checking: 'gurobi'
Error(s) in re-building vignettes:
--- re-building 'minimal_example.Rmd' using rmarkdown
Optimal solution found.
--- finished re-building 'minimal_example.Rmd'

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

--- re-building 'use_case_pilot_study.Rmd' using rmarkdown
Quitting from lines 42-45 (use_case_pilot_study.Rmd) 
Error: processing vignette 'use_case_pilot_study.Rmd' failed with diagnostics:
there is no package called 'readxl'
--- failed re-building 'use_case_pilot_study.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
Packages required but not available: 'haven', 'tibble'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggparty', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'usethis', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'ebayesthresh.Rmd' using rmarkdown
Quitting from lines 25-28 (ebayesthresh.Rmd) 
Error: processing vignette 'ebayesthresh.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ebayesthresh.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'fda'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'dplyr', 'ggplot2', 'sf', 'tidyr'

Packages suggested but not available for checking:
  'fields', 'rnaturalearth', 'smoothr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'separationplot', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mstate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'drc'

Packages suggested but not available for checking:
  'ggplot2', 'ggridges', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'ecb_sdw.Rmd' using rmarkdown
Quitting from lines 29-31 (ecb_sdw.Rmd) 
Error: processing vignette 'ecb_sdw.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ecb_sdw.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'Ecfun'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'rvest'

Packages suggested but not available for checking:
  'car', 'Ecdat', 'ipumsr', 'bayesplot', 'bssm', 'ggplot2', 'tibble',
  'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'broom'

Packages suggested but not available for checking:
  'tidyr', 'testthat', 'leaflet', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sf'
Error(s) in re-building vignettes:
--- re-building 'echo-vignette.Rmd' using rmarkdown
Quitting from lines 51-100 (echo-vignette.Rmd) 
Error: processing vignette 'echo-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'echo-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'readr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'ggspatial', 'httptest', 'kableExtra', 'sf',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geouy', 'haven', 'janitor', 'labelled', 'readxl', 'srvyr',
  'statar', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'WGCNA'

Packages suggested but not available for checking: 'factoextra', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.r'
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("ecmwfr")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'dplyr', 'EML', 'ggplot2', 'neonUtilities', 'tidyr'

Packages suggested but not available for checking:
  'ritis', 'taxize', 'testthat', 'worrms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sna'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'ggplot2', 'ggraph', 'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'alphahull', 'sf'
Package suggested but not available for checking: 'seacarb'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'intergraph', 'sna', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bipartite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'ggraph'
Error(s) in re-building vignettes:
--- re-building 'economiccomplexity.Rmd' using rmarkdown
   [[ suppressing 785 column names '0011', '0012', '0013' ... ]]
   [[ suppressing 785 column names '0011', '0012', '0013' ... ]]

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

computing product projection...
--------------------------------------------------
0 threshold...
0.05 threshold...
0.1 threshold...
0.15 threshold...
0.2 threshold...
0.25 threshold...
0.3 threshold...
0.35 threshold...
0.4 threshold...
0.45 threshold achieves the avg number of connections
computing product projection...
--------------------------------------------------
0 threshold...
0.05 threshold...
0.1 threshold...
0.15 threshold...
0.2 threshold...
0.25 threshold...
0.3 threshold...
0.35 threshold...
0.4 threshold...
0.45 threshold...
0.5 threshold...
0.55 threshold achieves the avg number of connections
Quitting from lines 122-144 (economiccomplexity.Rmd) 
Error: processing vignette 'economiccomplexity.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building 'economiccomplexity.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'bipartite'

Packages suggested but not available for checking:
  'readr', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'biomod2', 'rms'

Packages suggested but not available for checking: 'alphahull', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'GET'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'qgraph', 'philentropy'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'Hmisc', 'readr', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'smacof'
Error(s) in re-building vignettes:
--- re-building 'IntroductionETA.Rmd' using rmarkdown
Quitting from lines 201-211 (IntroductionETA.Rmd) 
Error: processing vignette 'IntroductionETA.Rmd' failed with diagnostics:
there is no package called 'smacof'
--- failed re-building 'IntroductionETA.Rmd'

--- re-building 'Transformation.Rmd' using rmarkdown
Quitting from lines 154-157 (Transformation.Rmd) 
Error: processing vignette 'Transformation.Rmd' failed with diagnostics:
there is no package called 'smacof'
--- failed re-building 'Transformation.Rmd'

SUMMARY: processing the following files failed:
  'IntroductionETA.Rmd' 'Transformation.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'ggraph', 'dplyr'
Running examples in 'ecpc-Ex.R' failed
The error most likely occurred in:

> ### Name: visualiseGroupset
> ### Title: Visualise a group set
> ### Aliases: visualiseGroupset
> 
> ### ** Examples
> 
> #groups without hierarchical constraints
> groupset <- list("Group1"=c(1:20),"Group2"=c(15,30))
> visualiseGroupset(groupset,c(0.5,2))
Loading required namespace: ggplot2
Failed with error:  'there is no package called 'ggplot2''
Loading required namespace: ggraph
Failed with error:  'there is no package called 'ggraph''
Loading required namespace: igraph
Loading required namespace: scales
Loading required namespace: dplyr
Failed with error:  'there is no package called 'dplyr''
Error in visualiseGroupset(groupset, c(0.5, 2)) : 
  Packages ggplot2, ggraph, igraph and scales should be installed
Execution halted
Packages required but not available: 'caret', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'dae', 'ggplot2', 'pbkrtest', 'tidyverse'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'spdep', 'sf', 'tibble', 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'eddington.Rmd' using rmarkdown
Quitting from lines 16-26 (eddington.Rmd) 
Error: processing vignette 'eddington.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'eddington.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'bupaR', 'dplyr', 'ggplot2', 'ggthemes', 'tibble', 'tidyr', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'lintr', 'httptest', 'devtools', 'dplyr', 'tidyr',
  'roxygen2', 'pkgdown'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'edgarWebR.Rmd' using rmarkdown
Quitting from lines 17-26 (edgarWebR.Rmd) 
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'edgarWebR.Rmd'

--- re-building 'parsing.Rmd' using rmarkdown
Quitting from lines 16-22 (parsing.Rmd) 
Error: processing vignette 'parsing.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'parsing.Rmd'

SUMMARY: processing the following files failed:
  'edgarWebR.Rmd' 'parsing.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'network', 'tidygraph'
Packages required but not available: 'tibble', 'dplyr', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'ndl'
Packages required but not available:
  'AdaptGauss', 'DistributionOptimization', 'ClusterR',
  'DataVisualizations', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'haven', 'readxl', 'tibble', 'WeMix', 'Dire'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'broom', 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'plotly', 'tidyr', 'colourpicker',
  'tibble'

Packages suggested but not available for checking:
  'testthat', 'purrrlyr', 'GGally', 'broom', 'readr', 'tidyverse',
  'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstanarm', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'nnfor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'viridis'

Packages suggested but not available for checking:
  'cdom', 'testthat', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'arm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'viridis'

Packages suggested but not available for checking: 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EFAtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'dplyr', 'cli', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'qgraph'
Error(s) in re-building vignettes:
--- re-building 'eff2-doc.Rmd' using rmarkdown
Quitting from lines 23-26 (eff2-doc.Rmd) 
Error: processing vignette 'eff2-doc.Rmd' failed with diagnostics:
there is no package called 'qgraph'
--- failed re-building 'eff2-doc.Rmd'

SUMMARY: processing the following file failed:
  'eff2-doc.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'afex', 'brms', 'car', 'dplyr', 'ggplot2', 'lmerTest', 'mediation',
  'rms', 'rstanarm', 'rstantools', 'see', 'testthat', 'tidymodels',
  'tidyr'
Package unavailable to check Rd xrefs: 'rstantools'
Packages suggested but not available for checking:
  'pbkrtest', 'heplots', 'car', 'alr4', 'robustlmm'
Error(s) in re-building vignettes:
--- re-building 'methods-supported-by-effects.Rnw' using knitr
kpsewhich: major issue: User/administrator updates are out-of-sync.
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'methods-supported-by-effects.Rnw'

--- re-building 'partial-residuals.Rnw' using knitr
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'partial-residuals.Rnw'

--- re-building 'predictor-effects-gallery.Rnw' using knitr
Quitting from lines 96-101 (predictor-effects-gallery.Rnw) 
Error: processing vignette 'predictor-effects-gallery.Rnw' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'predictor-effects-gallery.Rnw'

SUMMARY: processing the following file failed:
  'predictor-effects-gallery.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'broom', 'testthat', 'patrick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qgraph', 'semPlot', 'NetworkToolbox', 'dplyr', 'network', 'GGally'

Packages suggested but not available for checking:
  'kableExtra', 'ggpubr', 'ggplot2', 'OpenMx', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'StanHeaders'

Packages suggested but not available for checking:
  'eggCountsExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidygraph', 'srvyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'network', 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EGRET'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dataRetrieval', 'fields'

Packages suggested but not available for checking:
  'EGRETci', 'testthat', 'pkgdown', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'logistf', 'ggplot2'
Running examples in 'EHR-Ex.R' failed
The error most likely occurred in:

> ### Name: Logistf
> ### Title: Firth's penalized-likelihood logistic regression with more
> ###   decimal places of p-value than 'logistf' function in the R package
> ###   'logistf'
> ### Aliases: Logistf
> 
> ### ** Examples
> 
> data(dataPheWAS)
> fit <- Logistf(X264.3 ~ exposure + age + race + gender, data=dd)
Error: Logistf requires the logistf package, please install it.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ehr_vignette_01_mxr.Rmd' using rmarkdown
Quitting from lines 11-13 (ehr_vignette_01_mxr.Rmd) 
Error: processing vignette 'ehr_vignette_01_mxr.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ehr_vignette_01_mxr.Rmd'

--- re-building 'ehr_vignette_02_str.Rmd' using rmarkdown
--- finished re-building 'ehr_vignette_02_str.Rmd'

--- re-building 'ehr_vignette_03_DoseBuilding.Rmd' using rmarkdown
--- finished re-building 'ehr_vignette_03_DoseBuilding.Rmd'

--- re-building 'ehr_vignette_04_Build_PK_Oral.Rmd' using rmarkdown
--- finished re-building 'ehr_vignette_04_Build_PK_Oral.Rmd'

SUMMARY: processing the following file failed:
  'ehr_vignette_01_mxr.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'plotly', 'viridis'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'readxl'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'GA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wru', 'dplyr', 'ggplot2', 'overlapping', 'sf', 'tidyr', 'leaflet'

Packages suggested but not available for checking:
  'opencage', 'testthat', 'tigris'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'bench'
Packages required but not available: 'readxl', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking: 'testthat', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'DALEX', 'ggrepel', 'ggiraphExtra', 'iBreakDown', 'tidyr'

Package suggested but not available for checking: 'lightgbm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'forcats', 'dendextend', 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qgraph'

Package suggested but not available for checking: 'IsingSampler'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'haven', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'readODS', 'readxl', 'EnvStats', 'colourpicker'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'testthat'
Package unavailable to check Rd xrefs: 'EloRating'
Packages required but not available: 'sna', 'network'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DataCombine', 'ggplot2', 'lmerTest', 'sjstats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'usefun', 'readr', 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'dplyr', 'tidyr', 'tibble', 'rsample'

Packages suggested but not available for checking:
  'rstanarm', 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EMD', 'nnfor', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'HLMdiag', 'readODS', 'saeRobust', 'spdep'

Packages suggested but not available for checking: 'testthat', 'simFrame'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EMD'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'tidyr', 'dplyr', 'gganimate', 'testthat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'testthat', 'eixport', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'rdflib'
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'taxadb', 'tibble', 'testthat', 'EML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls to packages already attached by Depends:
  'clusterSim' 'earth'
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'clusterSim' 'earth'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking:
  'bayesplot', 'brms', 'car', 'ggplot2', 'mediation', 'pbkrtest',
  'lmerTest', 'testthat'

Packages which this enhances but not available for checking:
  'CARBayes', 'geepack', 'mice', 'rstanarm'
Running examples in 'emmeans-Ex.R' failed
The error most likely occurred in:

> ### Name: auto.noise
> ### Title: Auto Pollution Filter Noise
> ### Aliases: auto.noise
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # (Based on belief that noise/10 is in decibel units)
> noise.lm <- lm(noise/10 ~ size * type * side, data = auto.noise)
> 
> # Interaction plot of predictions
> emmip(noise.lm, type ~ size | side)
Error in .requireNS("ggplot2", "The 'ggplot' engine requires the 'ggplot2' package be installed.") : 
  The 'ggplot' engine requires the 'ggplot2' package be installed.
Calls: emmip -> emmip.default -> .requireNS -> fail
Execution halted
Packages suggested but not available for checking: 'GGally', 'ggplot2'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sampleSelection'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wrassp', 'dplyr', 'readr', 'tibble', 'tidyr', 'cli'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ACDm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'pillar', 'readr', 'testthat'
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'hopbyhop'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'rgdal' 'rgeos'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'robustHD'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'testthat', 'rangeModelMetadata'

Packages suggested but not available for checking:
  'spocc', 'sf', 'blockCV', 'devtools', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ENMeval', 'ggpubr', 'forcats'

Packages suggested but not available for checking:
  'testthat', 'leaflet', 'ecospat', 'caret', 'CalibratR', 'fields',
  'vip', 'pdp', 'fastshap', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'GLMs.Rmd' using rmarkdown
Quitting from lines 50-69 (GLMs.Rmd) 
Error: processing vignette 'GLMs.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'GLMs.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dendextend', 'ggplot2', 'ggdendro'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'EnsemblePCReg-Ex.R' failed
The error most likely occurred in:

> ### Name: epcreg.save
> ### Title: Custom Functions for Disk I/O in 'EnsemblePCReg' Package
> ### Aliases: epcreg.save epcreg.load
> 
> ### ** Examples
> 
> data(servo)
> myformula <- class~motor+screw+pgain+vgain
> perc.train <- 0.7
> index.train <- sample(1:nrow(servo), size = round(perc.train*nrow(servo)))
> data.train <- servo[index.train,]
> data.predict <- servo[-index.train,]
> est <- epcreg(myformula, data.train, ncores=2
+   , baselearner.control=epcreg.baselearner.control(
+     baselearners="knn"
+     , baselearner.configs = make.configs("knn"
+       , config.df = expand.grid(kernel = "rectangular"
+         , k = c(5, 10)))), filemethod = TRUE)
running in parallel mode, using 2 cores
CV training of base learners...
binding predictions from all base learners...finished
finished CV training of base learners
processing fold 1 of 5 
processing fold 2 of 5 
processing fold 3 of 5 
processing fold 4 of 5 
processing fold 5 of 5 
> epcreg.save(est, "somefile")
> rm(est) # alternatively, exit and re-launch R session
> est.loaded <- epcreg.load("somefile")
Error in epcreg.load("somefile") : 
  unexpected multiple directories in tar filepaths
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'ggforce', 'qwraps2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'RCurl' 'bitops' 'rjson'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'ggpubr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'drc', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test_envDocument.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'BiocParallel'

Packages suggested but not available for checking:
  'testthat', 'xcms', 'MSnbase', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'concaveman', 'fields'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testhat.R'
Running the tests in 'tests/testhat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'car'

Package suggested but not available for checking: 'openair'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplotify', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'epade-Ex.R' failed
The error most likely occurred in:

> ### Name: box.plot.wtd
> ### Title: weighted Boxplot
> ### Aliases: box.plot.wtd
> ### Keywords: boxplot
> 
> ### ** Examples
> 
> x<-rnorm(1000)
> g<-round(runif(1000))
> w<-abs(rnorm(1000))
> d<- data.frame(x, g, w)
> box.plot.wtd('x', 'g', w='w', data=d)
Error in library(Hmisc) : there is no package called 'Hmisc'
Calls: box.plot.wtd -> library
Execution halted
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 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/epanet2toolkit/epanet2toolkit.Rcheck/00install.out' for details.
Running 'testthat.r'
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > #*****************************************
  > #
  > # (C) Copyright IBM Corp. 2017
  > # Author: Ernesto Arandia & Bradley J Eck
  > #
  > #*****************************************
  > 
  > 
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'tidyverse'

Package suggested but not available for checking: 'ggcorrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'cowplot', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'timeROC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'readxl', 'janitor', 'questionr', 'tidyr',
  'readr', 'tidyverse', 'leaflet', 'rvest'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rvest', 'tidyr', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'incidence'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'ggridges', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'epicontacts', 'leaflet', 'ggmap', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'devtools', 'usethis', 'pkgdown', 'styler',
  'lintr', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'precrec', 'testthat', 'kableExtra'
Packages required but not available: 'dplyr', 'forcats', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'epidict'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'fields', 'forecast', 'imputeTS', 'statnet'
Packages required but not available:
  'networkDynamic', 'tergm', 'tergmLite', 'ergm', 'network', 'ggplot2'

Packages suggested but not available for checking: 'ndtv', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GA', 'ggplot2', 'vcfR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'ggplot2', 'patchwork', 'rstan', 'StanHeaders'

Packages suggested but not available for checking:
  'dplyr', 'EpiSoon', 'forecastHybrid', 'kableExtra', 'rnaturalearth',
  'rstantools', 'tidyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'mstate', 'popEpi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'tidyverse', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'epiR_RSurveillance.Rmd' using rmarkdown
--- finished re-building 'epiR_RSurveillance.Rmd'

--- re-building 'epiR_descriptive.Rmd' using rmarkdown
Loading required package: survival
Package epiR 2.0.33 is loaded
Type help(epi.about) for summary information
Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses


Quitting from lines 56-62 (epiR_descriptive.Rmd) 
Error: processing vignette 'epiR_descriptive.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'epiR_descriptive.Rmd'

--- re-building 'epiR_measures_of_association.Rmd' using rmarkdown
Quitting from lines 19-22 (epiR_measures_of_association.Rmd) 
Error: processing vignette 'epiR_measures_of_association.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'epiR_measures_of_association.Rmd'

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

--- re-building 'epiR_surveillance.Rmd' using rmarkdown
Quitting from lines 263-289 (epiR_surveillance.Rmd) 
Error: processing vignette 'epiR_surveillance.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'epiR_surveillance.Rmd'

SUMMARY: processing the following files failed:
  'epiR_descriptive.Rmd' 'epiR_measures_of_association.Rmd'
  'epiR_surveillance.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'ggdag'

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kableExtra'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'incidence'
Error(s) in re-building vignettes:
--- re-building 'epitrix.Rmd' using rmarkdown
Quitting from lines 122-133 (epitrix.Rmd) 
Error: processing vignette 'epitrix.Rmd' failed with diagnostics:
there is no package called 'incidence'
--- failed re-building 'epitrix.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'rtweet', 'readxl', 'tidyverse',
  'tidytext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cli'

Packages suggested but not available for checking: 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'usethis', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'testthat', 'TopKLists', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright 2019-2019 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of epsiwal.
  > #
  > # epsiwal is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # epsiwal is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with epsiwal.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2019-06-10
  > # Copyright: Steven E. Pav, 2019-2019
  > # Author: Steven E. Pav
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tibble', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'eplusr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'readxl', 'ggplot2', 'ggiraph', 'ggiraphExtra', 'FSA'
Error(s) in re-building vignettes:
--- re-building 'eq5d.Rmd' using rmarkdown
Quitting from lines 128-139 (eq5d.Rmd) 
Error: processing vignette 'eq5d.Rmd' failed with diagnostics:
there is no package called 'readxl'
--- failed re-building 'eq5d.Rmd'

SUMMARY: processing the following file failed:
  'eq5d.Rmd'

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'OpenMx'
Error(s) in re-building vignettes:
--- re-building 'equateIRT_tutorial.Rmd' using rmarkdown
Loading required package: MASS
Loading required package: msm
Loading required package: polycor
Quitting from lines 83-87 (equateIRT_tutorial.Rmd) 
Error: processing vignette 'equateIRT_tutorial.Rmd' failed with diagnostics:
there is no package called 'sna'
--- failed re-building 'equateIRT_tutorial.Rmd'

--- re-building 'equateIRT_paper.Rnw' using Sweave
Warning: Argument mod1 is deprecated; please use mods and which instead.
Warning: Argument mod2 is deprecated; please use mods and which instead.
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

--- finished re-building 'equateIRT_paper.Rnw'

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

Error: Vignette re-building failed.
In addition: Warning message:
In system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
Execution halted
Packages required but not available: 'broom', 'broom.mixed'

Packages suggested but not available for checking:
  'texPreview', 'testthat', 'forecast', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'PairedData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'cubature' 'rootSolve'
  All declared Imports should be used.
Package suggested but not available for checking: 'mzR'
Package required but not available: 'pillar'

Packages suggested but not available for checking:
  'tibble', 'testthat', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ergm', 'network', 'btergm', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ergm', 'egor', 'network', 'tibble', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ergm', 'network'

Package suggested but not available for checking: 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'network', 'tibble'

Packages suggested but not available for checking:
  'sna', 'latentnet', 'testthat', 'tergm', 'ergm.count',
  'ergm.userterms', 'networkDynamic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'network', 'ergm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'signal'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'rlang'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
Packages required but not available:
  'ggplot2', 'car', 'broom', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly'

Packages suggested but not available for checking: 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readODS', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'trialr', 'DiagrammeR', 'viridis'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sf'

Packages suggested but not available for checking:
  'colourpicker', 'leafem', 'leaflet', 'testthat', 'tmap', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'datamods', 'ggplot2'

Packages suggested but not available for checking:
  'rio', 'testthat', 'ggthemes', 'hrbrthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'haven', 'rvest', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'brms', 'dplyr', 'tidyr', 'ggplot2', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qgraph', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'autoimage'

Packages suggested but not available for checking:
  'readr', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'AER', 'ivpack', 'modelsummary', 'testthat', 'car'
Running examples in 'estimatr-Ex.R' failed
The error most likely occurred in:

> ### Name: lh_robust
> ### Title: Linear Hypothesis for Ordinary Least Squares with Robust
> ###   Standard Errors
> ### Aliases: lh_robust
> 
> ### ** Examples
> 
> 
> library(fabricatr)
> dat <- fabricate(
+   N = 40,
+   y = rpois(N, lambda = 4),
+   x = rnorm(N),
+   z = rbinom(N, 1, prob = 0.4),
+   clusterID = sample(1:4, 40, replace = TRUE)
+ )
> 
> # Default variance estimator is HC2 robust standard errors
> lhro <- lh_robust(y ~ x + z, data = dat, linear_hypothesis = "z + 2x = 0")
Loading required namespace: car
Failed with error:  'there is no package called 'car''
Error in loadNamespace(x) : there is no package called 'car'
Calls: lh_robust ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'sleep.R'
  Comparing 'sleep.Rout' to 'sleep.Rout.save' ... OK
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'Hmisc', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggalluvial', 'ggplot2', 'ggridges'

Packages suggested but not available for checking: 'broom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'janitor', 'readr', 'rvest', 'tibble', 'usethis'

Packages suggested but not available for checking:
  'dbplyr', 'ggplot2', 'testthat'

VignetteBuilder packages required for checking but not installed:
  'ggplot2', 'dplyr', 'dbplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'geepack'
Packages required but not available: 'dplyr', 'rvest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'rvest', 'readr'

Packages suggested but not available for checking: 'tidytext', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'readr'
Packages required but not available:
  'broom', 'dplyr', 'readr', 'sf', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'roxygen2', 'rvest', 'testthat', 'tmap', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'agricolae', 'car', 'dplyr', 'ggcorrplot', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'ggplot2', 'readr', 'readxl', 'tibble', 'tidyr',
  'viridis'

Packages suggested but not available for checking:
  'EnvStats', 'ggalt', 'forcats', 'mockery', 'shinytest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'MetaUtility', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'EnvStats'

Package suggested but not available for checking: 'SpatialExtremes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EventDetectR', 'plotly', 'ggplot2'

Packages suggested but not available for checking:
  'roxygen2', 'shinytest', 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'imputeTS', 'forecast', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

Packages suggested but not available for checking: 'testthat', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'testthat', 'dplyr', 'tidyr', 'tidyquant', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'rstanarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'EmpiricalCalibration', 'Cyclops'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'geomorph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rrepast', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'exactci'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'roxygen2', 'styler', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pkgbuild'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'dplyr', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'pkgload'
Running 'runit.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'revdbayes', 'testthat'
Package unavailable to check Rd xrefs: 'revdbayes'
Package required but not available: 'brms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rsamtools', 'GenomicAlignments', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'readr', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'httptest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'dplyr', 'ggplot2', 'kableExtra', 'rio'

Packages suggested but not available for checking: 'gapminder', 'devtools'

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.
Package suggested but not available for checking: 'smoof'
Package required but not available: 'semiArtificial'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggridges', 'lemon', 'mediation', 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'forcats', 'ggplot2', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'FactoMineR', 'GDAtools', 'quanteda', 'quanteda.textmodels',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spdep'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'repr', 'ggplot2', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'examples.Rmd' using rmarkdown
--- finished re-building 'examples.Rmd'

--- re-building 'labels-support.Rmd' using rmarkdown
Quitting from lines 113-121 (labels-support.Rmd) 
Error: processing vignette 'labels-support.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'labels-support.Rmd'

--- re-building 'tables-with-labels.Rmd' using rmarkdown
--- finished re-building 'tables-with-labels.Rmd'

--- re-building 'xlsx-export.Rmd' using rmarkdown
--- finished re-building 'xlsx-export.Rmd'

SUMMARY: processing the following file failed:
  'labels-support.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'numDeriv'
  All declared Imports should be used.
Packages required but not available: 'sf', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompRandFld', 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'exuberdata', 'forcats', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'readr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'pillar', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'eyedata', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'forestmodel', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'drc', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'GGally'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'haven', 'readxl', 'textreadr', 'tibble', 'mboxr', 'vroom', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'tsibble'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'tidyr', 'tsibbledata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggridges', 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'NMF'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fabletools', 'tsibble', 'prophet', 'dplyr', 'distributional'

Packages suggested but not available for checking:
  'tsibbledata', 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fabletools', 'dplyr', 'tsibble', 'tibble', 'tidyr', 'distributional'

Packages suggested but not available for checking:
  'feasts', 'forecast', 'testthat', 'tsibbledata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tsibble', 'tibble', 'ggplot2', 'dplyr', 'tidyr', 'distributional'

Packages suggested but not available for checking:
  'fable', 'pillar', 'feasts', 'testthat', 'tsibbledata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tibble', 'dplyr'
Error(s) in re-building vignettes:
--- re-building 'factiv.Rmd' using rmarkdown
Quitting from lines 84-85 (factiv.Rmd) 
Error: processing vignette 'factiv.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'factiv.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'dendextend', 'FactoMineR', 'ggpubr', 'ggrepel', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FactoMineR', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'ggplot2', 'ggrepel'

Packages suggested but not available for checking: 'missMDA', 'Factoshiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggpubr', 'agricolae', 'forcats'

Packages suggested but not available for checking: 'survminer', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'building_a_factory.Rmd' using rmarkdown
Quitting from lines 24-50 (building_a_factory.Rmd) 
Error: processing vignette 'building_a_factory.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'building_a_factory.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'FactoMineR', 'FactoInvestigate', 'ggplot2', 'colourpicker',
  'ggrepel', 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R6' 'caTools' 'httr' 'jsonlite' 'rlang'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'cowplot'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DALEX', 'ggplot2', 'patchwork', 'ggdendro', 'ggrepel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'devtools', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'cleanr', 'devtools', 'lintr', 'packager', 'pkgbuild', 'pkgload',
  'rasciidoc', 'roxygen2', 'testthat', 'usethis'

VignetteBuilder package required for checking but not installed: 'rasciidoc'
Namespace in Imports field not imported from: 'fritools'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'Building_Packages.Rmd'
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rasciidoc' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'Building_Packages.Rmd' using 'UTF-8'... failed to complete the test
Package required but not available: 'sensitivity'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tibble', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyhydat', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'sf'
Running examples in 'fasterize-Ex.R' failed
The error most likely occurred in:

> ### Name: fasterize
> ### Title: Rasterize an sf object of polygons
> ### Aliases: fasterize
> 
> ### ** Examples
> 
> library(sf)
Error in library(sf) : there is no package called 'sf'
Execution halted
Namespace in Imports field not imported from: 'RobustGaSP'
  All declared Imports should be used.
Packages required but not available: 'FactoClass', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
Package required but not available: 'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'fastpseudo-Ex.R' failed
The error most likely occurred in:

> ### Name: fast_pseudo_mean
> ### Title: Calculate pseudo-observations.
> ### Aliases: fast_pseudo_mean
> 
> ### ** Examples
> 
> # Dummy data
> 
> id <- c(1, 2, 3, 4)
> female <- c(0, 1, 1, 0)
> time <- c(23, 45, 38, 66)
> event <- c(1, 0, 0, 0)
> 
> # Compute pseudo-observations
> 
> pseudo = fast_pseudo_mean(time, event, 50)
> 
> # Create a data frame
> 
> test <- data.frame(id, female, pseudo)
> 
> # Fit a regression model
> 
> library(geepack)
Error in library(geepack) : there is no package called 'geepack'
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'rvest', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mosaic', 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'ggformula', 'mosaicCalc', 'tidyr', 'readr', 'Hmisc', 'car', 'alr3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'tidygraph'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following file(s) containing GNU extensions:
  inst/Rcgi/Makefile
  src/Rcgi/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
Packages required but not available: 'ggplot2', 'tibble'

Package suggested but not available for checking: 'AmesHousing'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'DESeq2'
Packages suggested but not available for checking:
  'dplyr', 'roxygen2', 'testthat', 'tibble', 'tidyr'
Packages unavailable to check Rd xrefs: 'dplyr', 'tidyr'
Running examples in 'fauxnaif-Ex.R' failed
The error most likely occurred in:

> ### Name: na_if_in
> ### Title: Convert values to NA
> ### Aliases: na_if_in na_if na_if_not
> 
> ### ** Examples
> 
> -1:10
 [1] -1  0  1  2  3  4  5  6  7  8  9 10
> # We can replace -1...
> # ... explicitly
> na_if_in(-1:10, -1)
 [1] NA  0  1  2  3  4  5  6  7  8  9 10
> # ... by specifying values to keep
> na_if_not(-1:10, 0:10)
 [1] NA  0  1  2  3  4  5  6  7  8  9 10
> # ... using a formula
> na_if_in(-1:10, ~ . < 0)
 [1] NA  0  1  2  3  4  5  6  7  8  9 10
> # ... or using a function
> na_if_in(-1:10, min)
 [1] NA  0  1  2  3  4  5  6  7  8  9 10
> 
> messy_string <- c("abc", "", "def", "NA", "ghi", 42, "jkl", "NULL", "mno")
> # We can replace unwanted values...
> # ... one at a time
> na_if_in(messy_string, "")
[1] "abc"  NA     "def"  "NA"   "ghi"  "42"   "jkl"  "NULL" "mno" 
> # ... or all at once
> na_if_in(messy_string, "", "NA", "NULL", 1:100)
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> na_if_in(messy_string, c("", "NA", "NULL", 1:100))
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> na_if_in(messy_string, list("", "NA", "NULL", 1:100))
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> # ... or using a clever formula
> grepl("[a-z]{3,}", messy_string)
[1]  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE
> na_if_not(messy_string, ~ grepl("[a-z]{3,}", .))
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> 
> # na_if_in() is particularly useful inside dplyr::mutate
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fauxnaif.Rmd' using rmarkdown
Error: processing vignette 'fauxnaif.Rmd' failed with diagnostics:
Printing 'tibble' without 'tibble' package available
--- failed re-building 'fauxnaif.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'roxygen2', 'cowplot', 'ggExtra', 'broom',
  'broom.mixed'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forcats', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'DataVisualizations'

Packages suggested but not available for checking:
  'ADPclust', 'DatabionicSwarm', 'subspace', 'parallelDist', 'plotly',
  'ProjectionBasedClustering', 'GeneralizedUmatrix', 'densityClust',
  'Spectrum', 'clustrd', 'smacof', 'dendextend', 'VarSelLCM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fda'

Packages suggested but not available for checking: 'testthat', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fdapace'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'ggplot2', 'doBy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'patchwork', 'fdapace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fds'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'fda', 'fields', 'ggplot2', 'refund', 'testthat'
Package unavailable to check Rd xrefs: 'refund'
Error(s) in re-building vignettes:
--- re-building 'FLAM_canada.Rnw' using knitr
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
This is FDboost 1.0-0. 
Quitting from lines 81-104 (FLAM_canada.Rnw) 
Error: processing vignette 'FLAM_canada.Rnw' failed with diagnostics:
there is no package called 'fda'
--- failed re-building 'FLAM_canada.Rnw'

--- re-building 'FLAM_fuel.Rnw' using knitr
UVVIS is not centered per column, inducing a non-centered effect.
NIR is not centered per column, inducing a non-centered effect.
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'FLAM_fuel.Rnw'

--- re-building 'FLAM_viscosity.Rnw' using knitr
Use a smooth offset.
Warning in mboost_fit(bl, response = response, weights = weights, offset = offset,  :
  response contains missing values;
 weights of corresponding observations are set to zero and thus these observations are not used for fitting
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'FLAM_viscosity.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'fds'
Running examples in 'fdcov-Ex.R' failed
The error most likely occurred in:

> ### Name: classifier-com
> ### Title: Functional data classifier via concentration inequalities
> ### Aliases: classifier-com classif.com predict.classif.com
> 
> ### ** Examples
> 
> ## Not run: 
> ##D  library(fds);
> ##D  # Setup training data
> ##D  dat1 = rbind( 
> ##D    t(aa$y[,1:100]), t(ao$y[,1:100]), t(dcl$y[,1:100]), 
> ##D    t(iy$y[,1:100]), t(sh$y[,1:100]) 
> ##D  );
> ##D  # Setup testing data
> ##D  dat2 = rbind( 
> ##D    t(aa$y[,101:400]), t(ao$y[,101:400]), t(dcl$y[,101:400]), 
> ##D    t(iy$y[,101:400]), t(sh$y[,101:400]) 
> ##D  );
> ##D  
> ##D  datgrp = gl(5,100);
> ##D  clCom = classif.com( datgrp, dat1 );
> ##D  grp = predict( clCom, dat2, LOADING=TRUE );
> ##D  acc = c(
> ##D    sum( grp[1:300]==1 ), sum( grp[301:600]==2 ), sum( grp[601:900]==3 ), 
> ##D    sum( grp[901:1200]==4 ), sum( grp[1201:1500]==5 )
> ##D  )/300;
> ##D  print(rbind(gl(5,1),signif(acc,3)));
> ## End(Not run)
> ## Don't show: 
>  library(fds);
Error in library(fds) : there is no package called 'fds'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 29-41 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'rainbow'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'ggnewscale', 'ggforce'
Packages required but not available: 'dplyr', 'ggplot2', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'caret', 'FactoMineR', 'questionr'

Package suggested but not available for checking: 'fds'

Package which this enhances but not available for checking: 'NMF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Fgmutils', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'mosaic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rainbow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GA', 'ggplot2', 'tibble', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fabletools', 'tibble', 'tsibble', 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'tsibbledata', 'pillar', 'testthat', 'fable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mlr'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'clustMixType', 'testthat', 'ClustImpute'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'caret', 'tibble', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'dplyr', 'tibble', 'cli', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'vroom'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'Hmisc', 'readr', 'tibble', 'dplyr', 'sf'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rvest', 'tidyr', 'tidytext'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'readr'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'curl' 'prettycode'
  All declared Imports should be used.
Packages required but not available: 'rstan', 'ggplot2', 'ergm', 'network'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gganimate', 'ggplot2', 'tibble', 'tourr', 'ggrepel',
  'ggforce', 'tidyr'

Packages suggested but not available for checking:
  'roxygen2', 'pkgdown', 'testthat', 'forcats', 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nls.multstart'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #library(ffbase)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running examples in 'FField-Ex.R' failed
The error most likely occurred in:

> ### Name: FField-package
> ### Title: Force field simulation for a set of points
> ### Aliases: FField FField-package
> ### Keywords: package
> 
> ### ** Examples
> 
> # Repel points
> coords <-
+   FFieldPtRep(coords = cbind(mtcars$wt * 100 / max(mtcars$wt), 
+                              mtcars$mpg * 100 / max(mtcars$mpg)),
+               rep.fact = 40)
> head(mtcars)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
> head(coords)
         x        y
1 45.11259 58.47014
2 54.19136 61.20140
3 40.34714 69.42976
4 62.48920 65.94822
5 59.81417 56.33633
6 66.54832 53.33343
>   
> # Demo
> FFieldPtRepDemo()
Error in library(ggplot2) : there is no package called 'ggplot2'
Calls: FFieldPtRepDemo -> library
Execution halted
Packages suggested but not available for checking: 'car', 'testthat'
Packages required but not available:
  'dplyr', 'forcats', 'ggdist', 'ggplot2', 'tibble', 'tidyr', 'usethis'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'httptest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ffscrapr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'forcats', 'ggplot2', 'ggridges', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jpmesh', 'readr', 'sf', 'stars', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fgeo.tool', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'fgeo.plot', 'ggplot2', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fgeo.tool', 'ggplot2', 'ggrepel'

Packages suggested but not available for checking:
  'fgeo.analyze', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'fgeo.analyze', 'fgeo.plot', 'fgeo.tool'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'tibble'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'network', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fdapace'

Package suggested but not available for checking: 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FGSG/FGSG.Rcheck/00install.out' for details.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'flexsurv', 'gapminder', 'GGally'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'golem', 'dplyr', 'ggplot2', 'plotly', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'ggplot2', 'concaveman'

Packages suggested but not available for checking:
  'kableExtra', 'RStoolbox'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'patchwork'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'dplyr'
Packages required but not available:
  'broom', 'dplyr', 'forcats', 'GGally', 'ggplot2', 'mice', 'pillar',
  'tidyr'

Packages suggested but not available for checking:
  'readr', 'rstan', 'survminer', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'readODS', 'readxl', 'testthat', 'tidyr'
Package required but not available: 'EML'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'diveRsity'
Package unavailable to check Rd xrefs: 'diveRsity'
Packages required but not available:
  'tune', 'cli', 'dials', 'dplyr', 'ggplot2', 'tibble', 'tidyr',
  'workflows', 'yardstick'

Packages suggested but not available for checking:
  'discrim', 'klaR', 'parsnip', 'recipes', 'rsample', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'klaR', 'ggplot2', 'GGally', 'Rcmdr', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'readr', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'dm', 'ggplot2', 'tidyr', 'DiagrammeR'
Error(s) in re-building vignettes:
--- re-building 'Data-Model.Rmd' using rmarkdown
Quitting from lines 18-27 (Data-Model.Rmd) 
Error: processing vignette 'Data-Model.Rmd' failed with diagnostics:
there is no package called 'dm'
--- failed re-building 'Data-Model.Rmd'

--- re-building 'fishdata-examples.Rmd' using rmarkdown
Quitting from lines 20-24 (fishdata-examples.Rmd) 
Error: processing vignette 'fishdata-examples.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'fishdata-examples.Rmd'

SUMMARY: processing the following files failed:
  'Data-Model.Rmd' 'fishdata-examples.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'dplyr', 'fishualize',
  'ggplot2', 'rfishbase', 'tidybayes', 'tidyr', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fda.usc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'respirometry'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rfishbase', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'community-analysis.Rmd' using rmarkdown
--- finished re-building 'community-analysis.Rmd'

--- re-building 'comparative-analysis.Rmd' using rmarkdown
Quitting from lines 41-48 (comparative-analysis.Rmd) 
Error: processing vignette 'comparative-analysis.Rmd' failed with diagnostics:
there is no package called 'rfishbase'
--- failed re-building 'comparative-analysis.Rmd'

SUMMARY: processing the following file failed:
  'comparative-analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'rfishbase', 'rnaturalearth', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'janitor', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'ggthemes'
Packages required but not available:
  'ggplot2', 'patchwork', 'viridis', 'ggthemes', 'varian', 'paletteer',
  'leaflet', 'sf', 'leafgl', 'exactextractr'

Packages suggested but not available for checking:
  'CopernicusDEM', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'Hmisc'
Package unavailable to check Rd xrefs: 'Hmisc'
Namespaces in Imports field not imported from:
  'MASS' 'XML' 'gglasso' 'methods'
  All declared Imports should be used.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'EnvStats', 'flexsurv', 'ihs', 'revdbayes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'rvest', 'tidyr', 'tibble', 'cli'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr', 'readr', 'tibble', 'broom', 'patchwork',
  'fivethirtyeightdata'
Running examples in 'fivethirtyeight-Ex.R' failed
The error most likely occurred in:

> ### Name: ahca_polls
> ### Title: American Health Care Act Polls
> ### Aliases: ahca_polls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # To convert data frame to tidy data (long) format, run:
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fivethirtyeight.Rmd' using rmarkdown
Some larger datasets need to be installed separately, like senators and
house_district_forecast. To install these, we recommend you install the
fivethirtyeightdata package by running:
install.packages('fivethirtyeightdata', repos =
'https://fivethirtyeightdata.github.io/drat/', type = 'source')
Quitting from lines 13-63 (fivethirtyeight.Rmd) 
Error: processing vignette 'fivethirtyeight.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'fivethirtyeight.Rmd'

--- re-building 'tame.Rmd' using rmarkdown
Quitting from lines 27-35 (tame.Rmd) 
Error: processing vignette 'tame.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'tame.Rmd'

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

SUMMARY: processing the following files failed:
  'fivethirtyeight.Rmd' 'tame.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgdown'
Namespaces in Imports field not imported from:
  'Rdpack' 'curl' 'mathjaxr'
  All declared Imports should be used.
Package required but not available: 'mlr'

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'plotly', 'smoof', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyr', 'eurostat', 'testthat'
Running examples in 'flagr-Ex.R' failed
The error most likely occurred in:

> ### Name: flag_divide
> ### Title: Assignment of the weights for the multiple flags
> ### Aliases: flag_divide
> 
> ### ** Examples
> 
> flags <- tidyr::spread(test_data[, c(1:3)], key = time, value = flags)
Error in loadNamespace(x) : there is no package called 'tidyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'flagr_introduction.Rmd' using rmarkdown
Quitting from lines 85-89 (flagr_introduction.Rmd) 
Error: processing vignette 'flagr_introduction.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'flagr_introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'mice', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'intro_to_AME.Rmd' using rmarkdown
Quitting from lines 65-66 (intro_to_AME.Rmd) 
Error: processing vignette 'intro_to_AME.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'intro_to_AME.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'ggplot2', 'ggforce', 'paletteer'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'cowplot', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'caret', 'moderndive', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'data.table' 'xtable'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'tibble', 'tidyr', 'readxl'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RCurl'
  All declared Imports should be used.
Package required but not available: 'ContaminatedMixt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'bayesplot', 'ggplot2', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Epi'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'smerc', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flexsurv'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mstate', 'tibble', 'tidyr', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'broom'
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'sf', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggsn', 'ggmap', 'ggplot2', 'GeoLight', 'fields'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'devtools', 'multipanelfigure', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'ggplot2', 'tibble'

Packages suggested but not available for checking: 'tidyverse', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TLMoments'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'BiodiversityR', 'cowplot', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'params', 'readr'

Package suggested but not available for checking: 'testthat'

Packages which this enhances but not available for checking:
  'ggplot2', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kableExtra'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'stats' 'utils'
  All declared Imports should be used.
Packages required but not available:
  'caret', 'FactoMineR', 'dplyr', 'factoextra', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'FMM-Ex.R' failed
The error most likely occurred in:

> ### Name: plotFMM
> ### Title: Plot fitted FMM models
> ### Aliases: plotFMM
> 
> ### ** Examples
> 
> 
> # Simulates an scenario in which an FMM model is suitable,
> res <- generateFMM(2,3,1.5,2.3,0.1,outvalues = TRUE,sigmaNoise = 0.3, plot=FALSE)
> # then a FMM model is fitted to the data.
> fit <- fitFMM(res$y, lengthAlphaGrid=20,lengthOmegaGrid=12)
Time difference of 0.245888 secs
> plotFMM(fit)
> 
> # Components plot of FMM Model fitted to neuronal data with various optional aesthetics
> data("neuronalSpike")
> fittedFMM2<-fitFMM(neuronalSpike, nback=2,
+                    lengthAlphaGrid = 24,lengthOmegaGrid = 10, numReps = 1)
|--------------------------------------------------|
|==================================================|
 Stopped by reaching maximum iterations (2 iteration(s) ) 
Time difference of 0.7228889 secs
> 
> plotFMM(fittedFMM2, components = TRUE)
> plotFMM(fittedFMM2, components = TRUE,
+         legendInComponentsPlot = FALSE,
+         textExtra = "Neuronal Data")
> 
> # With ggplot2, customizable plots can be created,
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages required but not available: 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'Epi'
Packages required but not available: 'rvest', 'tibble'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'ggplot2', 'sf', 'tidyr', 'dplyr', 'trip', 'patchwork'

Packages suggested but not available for checking: 'testthat', 'rworldmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'hrbrthemes', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'cowplot', 'tibble', 'tidyr', 'viridis', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'airportr', 'dplyr'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'dplyr', 'ggplot2', 'ggplotify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'doMC', 'testthat'
Packages required but not available: 'forecast', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'thief', 'ggplot2'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'dtplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'forecTheta', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'PSF', 'decomposedPSF', 'ggplot2', 'imputeTestbench', 'forecast'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GA', 'ggplot2', 'cowplot', 'fields'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'parsnip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'ggridges', 'sf', 'tibble', 'yardstick',
  'blockCV', 'forcats', 'patchwork'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'tidyr', 'broom', 'forcats',
  'tibble', 'systemfit', 'ggpmisc', 'car', 'FinCal', 'ggdendro'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'broom', 'tibble'

Package suggested but not available for checking: 'labelled'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'forestplot2_vtests.R'
  Running 'test_visual_w_cochrane_mdata.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library('testthat')
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'dplyr', 'viridis', 'tidyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > testthat::test_check("formulaic")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Running examples in 'forrel-Ex.R' failed
The error most likely occurred in:

> ### Name: MPPsims
> ### Title: Missing person power simulations
> ### Aliases: MPPsims
> 
> ### ** Examples
> 
> x = nuclearPed(fa = "Gf", mo = "Gm", children = c("Uncle", "Mother"), sex = 1:2)
> x = addChildren(x, fa = "Father", mo = "Mother", nch = 3, sex = c(1,2,1),
+                 id = c("S1", "S2", "MP"))
Father: Creating new individual with ID = Father
> x = addSon(x, "Father", id = "HS")
Mother: Creating new individual with ID = NN_1
> 
> # Brother S1 is already genotyped with a marker with 4 alleles
> m = marker(x, S1 = 1:2, alleles = 1:4)
> x = setMarkers(x, m)
> 
> # Alternatives for additional genotyping
> sel = list("Father", "S2", "HS", c("Gm", "Uncle"))
> 
> plot(x, marker = 1, hatched = sel)
> 
> # Simulate
> simData = MPPsims(x, selections = sel, nProfiles = 2, lrSims = 2)
Selection: Baseline
Selection: Father
Selection: S2
Selection: HS
Selection: Gm, Uncle
Total time used: 0.46 secs
> 
> # Power plot
> powerPlot(simData, type = 3)
Error: Package `ggplot2` is not installed. Please install this and try again.
Execution halted
Packages required but not available:
  'Distance', 'ggvoronoi', 'lidR', 'plotly', 'tidyr', 'vroom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'FactoMineR', 'forcats', 'ggplot2', 'likert', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'Overview.Rmd' using rmarkdown
Quitting from lines 25-33 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'RStoolbox', 'caret'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.r'
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("foto")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'fourierin_details.Rmd' using rmarkdown
Quitting from lines 50-83 (fourierin_details.Rmd) 
Error: processing vignette 'fourierin_details.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'fourierin_details.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'cli', 'expsmooth', 'fma', 'forecast', 'ggplot2'

Packages suggested but not available for checking:
  'GGally', 'Mcomp', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'fable', 'fabletools', 'feasts', 'ggplot2', 'tibble',
  'tidyr', 'tsibble', 'tsibbledata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'fma', 'expsmooth'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'forecast'
Packages suggested but not available for checking: 'ggplot2', 'dplyr'
Running examples in 'fractional-Ex.R' failed
The error most likely occurred in:

> ### Name: numerical
> ### Title: Convert a fractional object to the equivalent numeric object
> ### Aliases: numerical numerical.charFrac numerical.default
> ###   numerical.fractional
> 
> ### ** Examples
> 
> suppressPackageStartupMessages(library(dplyr))
Error in library(dplyr) : there is no package called 'dplyr'
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Theory.Rmd' using rmarkdown
Quitting from lines 18-26 (Theory.Rmd) 
Error: processing vignette 'Theory.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'Theory.Rmd'

--- re-building 'Vulgar_Fractions_in_R.Rmd' using rmarkdown
Quitting from lines 45-48 (Vulgar_Fractions_in_R.Rmd) 
Error: processing vignette 'Vulgar_Fractions_in_R.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'Vulgar_Fractions_in_R.Rmd'

SUMMARY: processing the following files failed:
  'Theory.Rmd' 'Vulgar_Fractions_in_R.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'netmeta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking: 'dplyr', 'plotly', 'egg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'doBy'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lamW'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Packages required but not available: 'fdadensity', 'fdapace'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'WGCNA'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fda'
Packages required but not available: 'ggplot2', 'GGally'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  + 	library(testthat)
  + 	library(frequencyConnectedness)
  + 	test_check("frequencyConnectedness")
  + }
  Error in packageVersion("testthat") : 
    there is no package called 'testthat'
  Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'haven', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

Packages suggested but not available for checking: 'survminer', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'packager', 'pkgload', 'testthat'
Package unavailable to check Rd xrefs: 'devtools'
Packages required but not available: 'dplyr', 'ggplot2', 'Hmisc', 'ggpubr'

Packages suggested but not available for checking:
  'dggrids', 'INLA', 'spdep', 'testthat', 'verification'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright 2016 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of fromo.
  > #
  > # fromo is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # fromo is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with fromo.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2016.03.25
  > # Copyright: Steven E. Pav, 2016-2016
  > # Author: Steven E. Pav
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 118-125 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building 'Introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'cna', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'FSA'
Packages required but not available: 'car', 'dplyr'

Packages suggested but not available for checking:
  'marked', 'pkgdown', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

Packages suggested but not available for checking:
  'arm', 'car', 'foba', 'Hmisc', 'klaR', 'rrlda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'testthat'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'RTCGA.rnaseq', 'ggplot2', 'tibble', 'lintr',
  'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'GA', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'googlesheets', 'readxl', 'readtext'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'randomForestSRC'

Package suggested but not available for checking: 'sparsevar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'pillar', 'tibble'
Packages suggested but not available for checking:
  'plotly', 'network', 'ggnetwork'
Error(s) in re-building vignettes:
--- re-building 'fssemR.Rmd' using rmarkdown
Quitting from lines 35-39 (fssemR.Rmd) 
Error: processing vignette 'fssemR.Rmd' failed with diagnostics:
there is no package called 'network'
--- failed re-building 'fssemR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > # required packages
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'forecast', 'rainbow', 'sde', 'fda'

Packages suggested but not available for checking: 'fds', 'meboot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'afex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rplos', 'rcrossref', 'microdemic', 'tibble'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'pubchunks'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'devtools', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'biclust', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fda', 'dplyr', 'ggplot2', 'tidyr', 'patchwork'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fda.usc', 'fda', 'ggplot2', 'ggpubr', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(functClust)
  > 
  > library(tools)
  > tools::undoc("functClust")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'fields'

Packages suggested but not available for checking:
  'fda', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'geometry'
  All declared Imports should be used.
Packages required but not available: 'fda', 'funFEM', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'ggplot2', 'dplyr', 'cli'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'broom', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggrepel', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tidytext'
Error(s) in re-building vignettes:
--- re-building 'new_distinctiveness.Rmd' using rmarkdown
Quitting from lines 131-139 (new_distinctiveness.Rmd) 
Error: processing vignette 'new_distinctiveness.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'new_distinctiveness.Rmd'

--- re-building 'rarity_indices.Rmd' using rmarkdown
Quitting from lines 281-341 (rarity_indices.Rmd) 
Error: processing vignette 'rarity_indices.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'rarity_indices.Rmd'

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

SUMMARY: processing the following files failed:
  'new_distinctiveness.Rmd' 'rarity_indices.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'covid19us', 'Ecdat', 'ggplot2', 'patchwork'
Error(s) in re-building vignettes:
--- re-building 'beales.Rmd' using rmarkdown
--- finished re-building 'beales.Rmd'

--- re-building 'trendtests.Rmd' using rmarkdown
Quitting from lines 52-63 (trendtests.Rmd) 
Error: processing vignette 'trendtests.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'trendtests.Rmd'

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

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

> ### Name: future_invoke_map
> ### Title: Invoke functions via futures
> ### Aliases: future_invoke_map future_invoke_map_chr future_invoke_map_dbl
> ###   future_invoke_map_int future_invoke_map_lgl future_invoke_map_raw
> ###   future_invoke_map_dfr future_invoke_map_dfc
> 
> ### ** Examples
> 
> 
> df <- dplyr::tibble(
+   f = c("runif", "rpois", "rnorm"),
+   params = list(
+     list(n = 10),
+     list(n = 5, lambda = 10),
+     list(n = 10, mean = -3, sd = 10)
+   )
+ )
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'attachment', 'cli', 'parsermd', 'rcmdcheck', 'roxygen2', 'tibble',
  'tidyr', 'usethis'

Packages suggested but not available for checking: 'pkgload', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'subgroup_fusion.Rmd' using rmarkdown
Quitting from lines 64-76 (subgroup_fusion.Rmd) 
Error: processing vignette 'subgroup_fusion.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'subgroup_fusion.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'FusionLearn.Rmd' using rmarkdown
Quitting from lines 37-45 (FusionLearn.Rmd) 
Error: processing vignette 'FusionLearn.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'FusionLearn.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'leaflet', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'sessioninfo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'WGCNA', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'readr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'markovchain'
Packages suggested but not available for checking: 'broom', 'modelsummary'
Error(s) in re-building vignettes:
--- re-building 'chart_themes.Rmd' using rmarkdown
g3viz: visualizing gene/genome/gentics data for fun.
  - Pfam (v33.1)
  - UniProt (date: 2020/08/24)

Any questions, please send emails to <g3viz.group@gmail.com> or post on GitHub <https://github.com/G3viz/g3viz/issues>.
Please send questions to cbioportal@googlegroups.com
--- finished re-building 'chart_themes.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 25-29 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'sf', 'ggmap', 'ggspatial', 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'kableExtra', 'tidyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'pkgdown', 'taxize', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'rtracklayer'

Packages suggested but not available for checking: 'Hmisc', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyjson', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'hrbrthemes', 'gganimate', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'forecast', 'Ecdat', 'car'
Error(s) in re-building vignettes:
--- re-building 'AirbagEffectiveness.Rmd' using rmarkdown
--- finished re-building 'AirbagEffectiveness.Rmd'

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

--- re-building 'resampling.Rmd' using rmarkdown
Quitting from lines 126-142 (resampling.Rmd) 
Error: processing vignette 'resampling.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'resampling.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'MASS' 'gamlss'
  All declared Imports should be used.
Running examples in 'gamlss.spatial-Ex.R' failed
The error most likely occurred in:

> ### Name: draw.polys
> ### Title: Additional supporting functions for random Markov fields
> ### Aliases: draw.polys polys2nb nb2prec polys2polys nb2nb
> ### Keywords: regression spatial
> 
> ### ** Examples
> 
> # bringing the required libraries
> library(spdep)
Error in library(spdep) : there is no package called 'spdep'
Execution halted
Package required but not available: 'robustHD'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'googleAnalyticsR', 'rvest', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'testthat', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tmap', 'sf'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'GAparsimony-Ex.R' failed
The error most likely occurred in:

> ### Name: ga_parsimony
> ### Title: GA-PARSIMONY
> ### Aliases: ga_parsimony show,ga_parsimony-method
> ###   print,ga_parsimony-method print,ga_parsimony-method numericOrNA
> ### Keywords: optimize
> 
> ### ** Examples
> 
> 
> #################################
> ### Example 1: Classification ###
> #################################
> 
> # This a toy example that shows how to search, for the *iris* database, 
> # a parsimony classification NNET model with 'GAparsimony' 
> # and 'caret' packages. Validation errors and iterations have been
> # reduced to speedup the process
> 
> library(GAparsimony)
> # Training and testing Datasets
> library(caret)
Error in library(caret) : there is no package called 'caret'
Execution halted
Packages required but not available: 'ggplot2', 'fields'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'cowplot', 'dplyr', 'ggplot2', 'haplo.stats', 'plotly', 'rms'
Package unavailable to check Rd xrefs: 'haplo.stats'
Error(s) in re-building vignettes:
--- re-building 'gap.Rnw' using Sweave
gap version 1.2.3-1
Loading required package: Matrix
Loading required package: quadprog
Loading required package: HaploSim
Loading required package: reshape

Attaching package: 'reshape'

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

    expand


Error: processing vignette 'gap.Rnw' failed with diagnostics:
 chunk 13 
Error in library(cowplot) : there is no package called 'cowplot'

--- failed re-building 'gap.Rnw'

--- re-building 'jss.Rnw' using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'jss.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'parsnip', 'dplyr', 'tibble', 'tidyr', 'dials'

Packages suggested but not available for checking:
  'tidymodels', 'tidyverse', 'modeltime', 'timetk', 'roxygen2',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vcfR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'ggplot2', 'GA'

Packages suggested but not available for checking:
  'yardstick', 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'rstan', 'StanHeaders', 'RcppParallel'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'rstantools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'metR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'rvest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'pdp', 'vip', 'viridis'
Packages unavailable to check Rd xrefs: 'viridis', 'pdp'
Packages required but not available: 'ggplot2', 'readr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'paleofire'
Namespace in Imports field not imported from: 'raster'
  All declared Imports should be used.
Package suggested but not available for checking: 'gcmr'
Package unavailable to check Rd xrefs: 'gcmr'
Running examples in 'GDAdata-Ex.R' failed
The error most likely occurred in:

> ### Name: Decathlon
> ### Title: Top performances in the Decathlon from 1985 to 2006.
> ### Aliases: Decathlon
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Decathlon, package="GDAdata")
> summary(Decathlon[, grep("P.*", names(Decathlon))])
   Polevault         P100m             Plj              Psp       
 Min.   :2.850   Min.   : 597.0   Min.   : 569.0   Min.   :418.0  
 1st Qu.:4.200   1st Qu.: 765.0   1st Qu.: 757.0   1st Qu.:622.0  
 Median :4.400   Median : 806.0   Median : 804.0   Median :672.0  
 Mean   :4.405   Mean   : 806.6   Mean   : 807.4   Mean   :674.6  
 3rd Qu.:4.650   3rd Qu.: 847.0   3rd Qu.: 857.0   3rd Qu.:726.0  
 Max.   :5.760   Max.   :1042.0   Max.   :1089.0   Max.   :941.0  
      Phj           P400m         P110h             Ppv              Pdt       
 Min.   : 396   Min.   :532   Min.   : 526.0   Min.   : 321.0   Min.   :231.0  
 1st Qu.: 696   1st Qu.:746   1st Qu.: 777.0   1st Qu.: 673.0   1st Qu.:600.0  
 Median : 749   Median :789   Median : 824.0   Median : 731.0   Median :655.0  
 Mean   : 749   Mean   :788   Mean   : 821.6   Mean   : 734.4   Mean   :657.8  
 3rd Qu.: 803   3rd Qu.:832   3rd Qu.: 868.0   3rd Qu.: 804.0   3rd Qu.:713.0  
 Max.   :1061   Max.   :998   Max.   :1044.0   Max.   :1152.0   Max.   :970.0  
      Pjt             P1500      
 Min.   : 330.0   Min.   :121.0  
 1st Qu.: 588.0   1st Qu.:607.0  
 Median : 644.0   Median :669.0  
 Mean   : 648.1   Mean   :661.7  
 3rd Qu.: 707.0   3rd Qu.:725.0  
 Max.   :1040.0   Max.   :946.0  
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: 'stars', 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gdalcubes/gdalcubes.Rcheck/00install.out' for details.
Packages required but not available:
  'FactoMineR', 'ggplot2', 'ggrepel', 'GGally'

Package suggested but not available for checking: 'WeightedCluster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'leaflet', 'ggplot2', 'dplyr', 'readr', 'rgbif'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'badger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'gdxrrw', 'testthat'
Package required but not available: 'autoimage'

Packages suggested but not available for checking:
  'sf', 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'geepack', 'testthat'
Package required but not available: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'AER', 'ivpack', 'geepack'
Namespace in Imports field not imported from: 'rootSolve'
  All declared Imports should be used.
Packages required but not available: 'Hmisc', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'readr'
Running examples in 'gemma2-Ex.R' failed
The error most likely occurred in:

> ### Name: calc_XHiY
> ### Title: Calculate XHiY
> ### Aliases: calc_XHiY
> 
> ### ** Examples
> 
> readr::read_tsv(system.file("extdata",
+ "mouse100.pheno.txt",
+ package = "gemma2"),
+ col_names = FALSE) -> pheno
Error in loadNamespace(x) : there is no package called 'readr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'compare-with-GEMMAv096.Rmd' using rmarkdown
Quitting from lines 74-78 (compare-with-GEMMAv096.Rmd) 
Error: processing vignette 'compare-with-GEMMAv096.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building 'compare-with-GEMMAv096.Rmd'

SUMMARY: processing the following file failed:
  'compare-with-GEMMAv096.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (c) 2020, ETH Zurich
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggnetwork', 'ggplot2', 'ggraph', 'network', 'ggseqlogo', 'ggtree',
  'dplyr', 'ShortRead'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'genderdata', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'GEOquery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'meboot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'DataVisualizations', 'fields', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'pkgload', 'testthat', 'tibble'
Namespace in Imports field not imported from: 'htmlwidgets'
  All declared Imports should be used.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exactextractr', 'spdep', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EnvStats', 'ggplot2', 'ssdtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tibble', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rvest', 'tidyr', 'tibble', 'tidytext'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rvest', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'geno2proteo-Ex.R' failed
The error most likely occurred in:

> ### Name: generatingCDSaaFile
> ### Title: Generating a file containing the DNA and AA sequences of all the
> ###   protein coding regions (CDSs) in a genome
> ### Aliases: generatingCDSaaFile
> 
> ### ** Examples
> 
>     # the data folder in this package
>     dataFolder = system.file("extdata", package="geno2proteo") 
> 
>     geneticCodeFile_line = file.path(dataFolder, 
+                                     "geneticCode_standardTable_lines.txt")
>     gtfFile = file.path(dataFolder, 
+                 "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
>     DNAfastaFile =  file.path(dataFolder, 
+             "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
>     
>     outputFolder = tempdir(); # using the current folder as output folder
>     # calling the function.
>     generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line, 
+         gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements
Calls: generatingCDSaaFile -> read.table -> scan
Execution halted
Running 'runTests.R'
Running the tests in 'tests/runTests.R' failed.
Complete output:
  > BiocGenerics:::testPackage("geno2proteo")
  Timing stopped at: 1.45 0.07 2.92
  Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 7 elements
  Timing stopped at: 0.12 0.03 0.34
  Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 13 elements
  
  
  RUNIT TEST PROTOCOL -- Wed Aug  4 22:34:57 2021 
  *********************************************** 
  Number of test functions: 6 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  geno2proteo RUnit Tests - 6 test functions, 2 errors, 0 failures
  ERROR in test_generatingCDSaaFile: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 7 elements
  ERROR in test_genomicLocsToWholeDNASequence: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 13 elements
  
  Test files with failing tests
  
     test_functionsInGeno2proteo.R 
       test_generatingCDSaaFile 
       test_genomicLocsToWholeDNASequence 
  
  
  Error in BiocGenerics:::testPackage("geno2proteo") : 
    unit tests failed for package geno2proteo
  Execution halted
Errors in running code in vignettes:
when running code in 'geno2proteoIntroduction.Rnw'

> options(width = 72)

> library(geno2proteo)

> dataFolder = system.file("extdata", package = "geno2proteo")

> geneticCodeFile = file.path(dataFolder, "geneticCode_standardTable_lines.txt")

> gtfFile_chr16 = file.path(dataFolder, "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")

> DNAfastaFile_chr16 = file.path(dataFolder, "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")

> tmpFolder = tempdir()

> generatingCDSaaFile(geneticCodeFile_line = geneticCodeFile, 
+     gtfFile = gtfFile_chr16, DNAfastaFile = DNAfastaFile_chr16, 
+     outputFolder = .... [TRUNCATED] 

  When sourcing 'geno2proteoIntroduction.R':
Error: line 2 did not have 7 elements
Execution halted

  'geno2proteoIntroduction.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'geno2proteoIntroduction.Rnw' using Sweave

Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
 chunk 3 (label = example_generatingCDSaaFile) 
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements

--- failed re-building 'geno2proteoIntroduction.Rnw'

SUMMARY: processing the following file failed:
  'geno2proteoIntroduction.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'leaflet', 'dplyr', 'tidyr', 'ggplot2', 'tibble', 'forcats', 'readr',
  'rio'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggridges', 'hierfstat', 'RcppParallel', 'tibble', 'vcfR'

Packages suggested but not available for checking:
  'dplyr', 'junctions', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SOMbrero', 'plotly', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'sf'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'mapview', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'spdep', 'reldist', 'dplyr', 'broom'

Packages suggested but not available for checking:
  'ClustGeo', 'car', 'ggpubr', 'kableExtra', 'viridis', 'testthat',
  'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'dplyr', 'tibble', 'leafpop', 'leaflet', 'mapview'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'maptools' 'rgdal' 'rgeos'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'readr', 'tibble', 'tidyr', 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rnaturalearth', 'sf', 'ggrepel', 'geogrid'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sf'

Packages suggested but not available for checking:
  'geofacet', 'ggplot2', 'ggrepel', 'httptest', 'janitor', 'leaflet',
  'testthat', 'tidyr', 'patchwork', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'geohashTools-Ex.R' failed
The error most likely occurred in:

> ### Name: gis_tools
> ### Title: Helpers for interfacing geohashes with sp/sf objects
> ### Aliases: gh_to_sp gh_to_spdf gh_to_spdf.default gh_to_spdf.data.frame
> ###   gh_to_sf gh_covering
> 
> ### ** Examples
> 
>   # get the neighborhood of this geohash in downtown Apia as an sp object
>   downtown = '2jtc5x'
>   apia_nbhd = unlist(gh_neighbors(downtown))
>   apia_sp = gh_to_sp(apia_nbhd)
> 
>   # all geohashes covering a random sampling within Apia:
>   apia_covering = gh_covering(smp <- sp::spsample(apia_sp, 10L, 'random'))
Warning in proj4string(obj) :
  CRS object has comment, which is lost in output
Warning in sp::proj4string(SP) :
  CRS object has comment, which is lost in output
Warning in spTransform(xSP, CRSobj, ...) :
  NULL source CRS comment, falling back to PROJ string
Warning in wkt(obj) : CRS object has no comment
> 
>   apia_sf = gh_to_sf(apia_nbhd)
Error in check_suggested("sf") : 
  This function requires an installation of sf; install.packages('sf') to proceed.
Calls: gh_to_sf -> check_suggested
Execution halted
Packages required but not available: 'sf', 'readr'

Packages suggested but not available for checking:
  'gistr', 'testthat', 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tibble', 'testthat', 'sf'
Running examples in 'geojson-Ex.R' failed
The error most likely occurred in:

> ### Name: feature
> ### Title: feature class
> ### Aliases: feature
> 
> ### ** Examples
> 
> # point -> feature
> x <- '{ "type": "Point", "coordinates": [100.0, 0.0] }'
> point(x) %>% feature()
<Feature> 
  type:  Point 
  coordinates:  [100,0] 
> 
> # multipoint -> feature
> x <- '{"type": "MultiPoint", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> multipoint(x) %>% feature()
<Feature> 
  type:  MultiPoint 
  coordinates:  [[100,0],[101,1]] 
> 
> # linestring -> feature
> x <- '{ "type": "LineString", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> linestring(x) %>% feature()
<Feature> 
  type:  LineString 
  coordinates:  [[100,0],[101,1]] 
> 
> # multilinestring -> feature
> x <- '{ "type": "MultiLineString",
+  "coordinates": [ [ [100.0, 0.0], [101.0, 1.0] ], [ [102.0, 2.0], [103.0, 3.0] ] ] }'
> multilinestring(x) %>% feature()
<Feature> 
  type:  MultiLineString 
  coordinates:  [[[100,0],[101,1]],[[102,2],[103,3]]] 
> 
> # add to a data.frame
> library('tibble')
Error in library("tibble") : there is no package called 'tibble'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'geojson-operations.Rmd' using rmarkdown

Attaching package: 'geojson'

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

    polygon

Quitting from lines 147-149 (geojson-operations.Rmd) 
Error: processing vignette 'geojson-operations.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'geojson-operations.Rmd'

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

SUMMARY: processing the following file failed:
  'geojson-operations.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggmap', 'dplyr', 'ggplot2'
Packages required but not available:
  'dplyr', 'nngeo', 'sf', 'tibble', 'tidycensus', 'tidyr', 'tigris',
  'ggplot2', 'readr', 'spdep'

Packages suggested but not available for checking: 'redist', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'GEOmap'
Package required but not available: 'fields'

Package suggested but not available for checking: 'RFOC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'inlmisc', 'spdep', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sf', 'EML', 'testthat', 'roxygen2'
Running examples in 'geometa-Ex.R' failed
The error most likely occurred in:

> ### Name: ISOImageryGCP
> ### Title: ISOImageryGCPCollection
> ### Aliases: ISOImageryGCP
> ### Keywords: ISO collection gcp imagery
> 
> ### ** Examples
> 
>   md <- ISOImageryGCP$new()
>   require(sf)
Loading required package: sf
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'sf'
>   pt <- sf::st_point(c(1,1))
Error in loadNamespace(x) : there is no package called 'sf'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'dplyr', 'readr', 'sf', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RRPP', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'devtools', 'ggmap', 'mapview', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RFOC', 'GEOmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'velociraptr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mapview'
Running examples in 'geosed-Ex.R' failed
The error most likely occurred in:

> ### Name: geo_midpoint
> ### Title: Point of Equidistance to Up to Three Longitude, Latitude Points
> ### Aliases: geo_midpoint
> ### Keywords: circle disk enclosing geo latitude longitude sed smallest
> 
> ### ** Examples
> 
> 
> # Load required packages
> require(mapview)
Loading required package: mapview
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'mapview'
> require(sp)
Loading required package: sp
> 
> # Create sample geo dataset
> sample_coord <-
+    matrix(
+         c(
+             sample(327131680:419648450, 3) / 10000000,
+             sample(-1147301410:-1241938690, 3) / 10000000
+         ),
+         ncol = 2
+     )
> 
> # Generate circumcenter and radius
> gmp <- geo_midpoint(sample_coord)
> 
> # Find distance to circumcenter
> radius <- geo_point_dist(rbind(sample_coord[1, ], gmp))
> 
> # Create 80 sided polygon based on gmp's center and radius
> gmp_poly <- geo_surround_poly(gmp, radius, 80)
> 
> # Join all the points into a single matrix
> bound_poly <- rbind(sample_coord, as.vector(gmp), gmp_poly)
> 
> # Create SpacialPoints object and pass to mapview for visualization
> mapview(
+     SpatialPoints(
+         bound_poly[,c(2, 1)],
+         proj4string = CRS("+proj=longlat +datum=WGS84")
+     )
+ )
Error in mapview(SpatialPoints(bound_poly[, c(2, 1)], proj4string = CRS("+proj=longlat +datum=WGS84"))) : 
  could not find function "mapview"
Execution halted
Packages required but not available: 'sparklyr', 'dplyr', 'dbplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'StatMatch', 'fields', 'geospt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'sf', 'wkutils'
Packages unavailable to check Rd xrefs: 'wkutils', 'sf'
Packages suggested but not available for checking:
  'DESeq2', 'ChAMP', 'tidyr', 'clusterProfiler'
Error(s) in re-building vignettes:
--- re-building 'GeoTcgaData.Rmd' using rmarkdown
Quitting from lines 283-287 (GeoTcgaData.Rmd) 
Error: processing vignette 'GeoTcgaData.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
--- failed re-building 'GeoTcgaData.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tidyr', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'iterators' 'methods'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'ggspatial', 'sf', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'readr', 'tibble', 'sf', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tourr', 'roxygen2', 'testthat'
Packages suggested but not available for checking:
  'dplyr', 'mice', 'testthat'
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'agricolae', 'ggplot2', 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: 'inti'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'ggplot2', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'libgit2.R'
  Comparing 'libgit2.Rout' to 'libgit2.Rout.save' ...4,6d3
< Linking to libgit2 v1.1.0, ssh support: YES
< No global .gitconfig found in: C:\Users\tomas
< No default user configured
  Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rio', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DataCombine', 'tidyr', 'tibble', 'rsample'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'roxygen2', 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'rvest', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'devtools'
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_getDTeval.Rmd' using rmarkdown
Quitting from lines 157-166 (Introduction_to_getDTeval.Rmd) 
Error: processing vignette 'Introduction_to_getDTeval.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'Introduction_to_getDTeval.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'readr', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'janitor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'fda', 'fda.usc', 'patchwork', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'tidyr', 'rvest'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'TeachingSampling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'tidyr', 'scatterpie', 'ggplot2', 'ggrepel', 'googlesheets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forcats'

Packages suggested but not available for checking:
  'lmerTest', 'testthat', 'AOV1R', 'GGally', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

Package suggested but not available for checking: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'babynames', 'sessioninfo', 'ggrepel', 'ggfittext',
  'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'forcats', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'broom.helpers', 'ggforce', 'Hmisc', 'intergraph',
  'labelled', 'network', 'sna', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble', 'plotly'

Packages suggested but not available for checking: 'testthat', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'flexsurv'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'transformr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'broom', 'corrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggplotify', 'aplot'

Package suggested but not available for checking: 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'patchwork'

Packages suggested but not available for checking:
  'gapminder', 'lintr', 'tibble', 'tidyr', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'forcats', 'ggraph', 'ggrepel', 'pillar',
  'tibble', 'tidygraph'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'do', 'set', 'rms', 'base.rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tibble', 'distributional'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'broom', 'modelr', 'cowplot', 'fda', 'forcats',
  'tidyr', 'posterior', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'labelled', 'patchwork', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'colourpicker'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'AER', 'brms', 'geepack', 'ggplot2', 'haven', 'logistf', 'mice',
  'rms', 'rstanarm', 'rstantools', 'see', 'sjstats', 'sjmisc',
  'testthat'
Running examples in 'ggeffects-Ex.R' failed
The error most likely occurred in:

> ### Name: ggeffect
> ### Title: Marginal effects, adjusted predictions and estimated marginal
> ###   means from regression models
> ### Aliases: ggeffect ggemmeans ggpredict
> 
> ### ** Examples
> 
> library(sjlabelled)
> data(efc)
> fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)
> 
> ggpredict(fit, terms = "c12hour")
# Predicted values of Total score BARTHEL INDEX

c12hour | Predicted |         95% CI
------------------------------------
      0 |     75.44 | [73.26, 77.63]
     20 |     70.38 | [68.56, 72.19]
     45 |     64.05 | [62.39, 65.70]
     65 |     58.98 | [57.16, 60.80]
     85 |     53.91 | [51.71, 56.11]
    105 |     48.85 | [46.15, 51.55]
    125 |     43.78 | [40.52, 47.05]
    170 |     32.38 | [27.73, 37.03]

Adjusted for:
*  neg_c_7 = 11.84
*  c161sex =  1.76
* c172code =  1.97
> ggpredict(fit, terms = c("c12hour", "c172code"))
Error in set_labels_helper(x = .dat, labels = labels, force.labels = force.labels,  : 
  Package 'haven' required for this function. Please install it.
Calls: ggpredict ... .add_labels_to_groupvariable -> <Anonymous> -> set_labels_helper
Execution halted
Packages required but not available: 'ggplot2', 'plotly', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'zeitgebr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'colourpicker', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'rstan'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'sessioninfo', 'concaveman'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggstance', 'ggridges', 'mosaicCore', 'tibble', 'ggforce',
  'labelled'

Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'mosaic', 'testthat', 'vdiffr', 'broom', 'sf',
  'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'forecast', 'ggrepel', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggfittext'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'ggdendro', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'aplot', 'factoextra', 'tibble', 'ggpubr', 'tidyr',
  'patchwork'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggrepel', 'tibble'

Packages suggested but not available for checking:
  'sf', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggplotify', 'tibble'

Package suggested but not available for checking: 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tibble'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggiraph', 'sjmisc', 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'ggforce', 'moonBook', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'sf', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'unisensR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggridges', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'GGally'

Package suggested but not available for checking: 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GGally', 'network', 'sna', 'ggplot2', 'GGMncv'

Package suggested but not available for checking: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'productplots', 'dplyr', 'plotly', 'tidyr', 'ggrepel'

Package suggested but not available for checking: 'patchwork'

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.
Packages required but not available:
  'ggplot2', 'tidyr', 'aplot', 'ggalt', 'ggforce', 'dplyr'

Packages suggested but not available for checking:
  'ggtreeExtra', 'ggtree', 'cowplot', 'readxl', 'ggnewscale',
  'kableExtra', 'gggenes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'GGMselect-Ex.R' failed
The error most likely occurred in:

> ### Name: selectFast
> ### Title: Estimate a graph in a Gaussian Graphical Model: Fast procedure
> ### Aliases: selectFast
> ### Keywords: multivariate graphs models
> 
> ### ** Examples
> 
> p=30
> n=30
> # simulate graph
> eta=0.11
> Gr <- simulateGraph(p,eta)
> # simulate data
> X <- rmvnorm(n, mean=rep(0,p), sigma=Gr$C)
> # estimate graph
> GRest <- selectFast(X, family="C01")
> 
> # plot result
> library(network)
Error in library(network) : there is no package called 'network'
Execution halted
Errors in running code in vignettes:
when running code in 'Notice.Rnw'

> library("GGMselect")
Loading required package: mvtnorm

> p = 30

> n = 30

> eta = 0.11

> Gr <- simulateGraph(p, eta)

> X <- rmvnorm(n, mean = rep(0, p), sigma = Gr$C)

> GRest <- selectFast(X, family = "C01")

> library(network)

  When sourcing 'Notice.R':
Error: there is no package called 'network'
Execution halted

  'Notice.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'Notice.Rnw' using Sweave
Loading required package: mvtnorm

Error: processing vignette 'Notice.Rnw' failed with diagnostics:
 chunk 2 
Error in library(network) : there is no package called 'network'

--- failed re-building 'Notice.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'tibble', 'testthat', 'tidyverse', 'nycflights13'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'network', 'sna'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'ggforce', 'gganimate'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidytext'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'tidyr', 'testthat', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'AER', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'Hmisc', 'sf', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'ggplot2', 'dplyr', 'tibble', 'ggthemes', 'moonBook',
  'editData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotly', 'ggplot2', 'readr', 'haven', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'aplot', 'cowplot', 'ggimage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpp', 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'ggrepel', 'broom', 'broom.mixed', 'gginnards'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'GGally', 'tidyr', 'dplyr', 'readr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'nlmixr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'viridis', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tibble', 'dplyr'

Packages suggested but not available for checking: 'gginnards', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggbeeswarm', 'ggnewscale', 'patchwork', 'rstatix', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'ggsci', 'tidyr', 'dplyr', 'cowplot',
  'ggsignif', 'rstatix', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colourpicker', 'dplyr', 'GGally', 'ggbeeswarm', 'ggplot2',
  'ggpmisc', 'ggrepel', 'ggstance', 'ggpubr', 'Hmisc', 'plotly',
  'survminer', 'tidyr', 'shinyFiles'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'ggmap', 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randomForestSRC', 'ggplot2', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggforce', 'ggrepel', 'viridis', 'tidygraph'

Packages suggested but not available for checking:
  'network', 'tibble', 'gganimate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'bgmm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggbeeswarm'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'ggbeeswarm', 'dplyr', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'ggplot2', 'plotly', 'qqplotr'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'lmerTest', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CVglasso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'patchwork', 'forcats', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'plotly', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'testthat', 'vdiffr', 'ggdendro', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'sf', 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking: 'ggmap', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'tibble'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggrepel', 'stars', 'vdiffr', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'photobiology', 'ggplot2', 'photobiologyWavebands', 'ggrepel',
  'dplyr', 'tidyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'Hmisc', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'ggsignif', 'ipmisc',
  'pairwiseComparisons', 'paletteer', 'patchwork', 'statsExpressions',
  'tidyr'

Packages suggested but not available for checking:
  'afex', 'forcats', 'ggcorrplot', 'ggExtra', 'metaBMA', 'testthat',
  'tibble', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'cowplot', 'dplyr', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'lintr', 'testthat', 'tidyr', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'ggplot2', 'dplyr', 'tibble', 'plotly', 'RVenn'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'ggmap', 'dplyr', 'testthat', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'ggrepel', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'class'
  All declared Imports should be used.
Package required but not available: 'refund'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat', 'cowplot', 'codemetar'
Error(s) in re-building vignettes:
--- re-building 'ghibli.Rmd' using rmarkdown
Loading required package: ghibli
Quitting from lines 43-53 (ghibli.Rmd) 
Error: processing vignette 'ghibli.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ghibli.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'cli'

Packages suggested but not available for checking: 'mockery', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'gapminder'
Running examples in 'gifti-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_binary_datatype
> ### Title: Convert Binary Data Type
> ### Aliases: convert_binary_datatype
> 
> ### ** Examples
> 
> convert_binary_datatype()
$size
[1] 1

$what
integer(0)

> convert_binary_datatype('NIFTI_TYPE_INT32')
$size
[1] 4

$what
integer(0)

> testthat::expect_error(convert_binary_datatype('NIFTI_TYPE_BLAH'))
Error in loadNamespace(x) : there is no package called 'testthat'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GIFTr_tutorial.Rmd' using rmarkdown
Quitting from lines 34-39 (GIFTr_tutorial.Rmd) 
Error: processing vignette 'GIFTr_tutorial.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'GIFTr_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'dynutils', 'readr', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qgraph', 'MIIVsem', 'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'lwgeom'

Package suggested but not available for checking: 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'efficiency.Rmd' using rmarkdown
Quitting from lines 17-120 (efficiency.Rmd) 
Error: processing vignette 'efficiency.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'efficiency.Rmd'

--- re-building 'plain_text.Rmd' using rmarkdown
Warning: No sorting applied.
Sorting is strongly recommended in combination with version control.
Warning: No sorting applied.
Sorting is strongly recommended in combination with version control.
Warning: No sorting applied.
Sorting is strongly recommended in combination with version control.
Warning: No sorting applied.
Sorting is strongly recommended in combination with version control.
Warning: No sorting applied.
Sorting is strongly recommended in combination with version control.
Warning: No sorting applied.
Sorting is strongly recommended in combination with version control.
Warning: No sorting applied.
Sorting is strongly recommended in combination with version control.
Warning: Changes in the metadata may lead to unnecessarily large diffs.
See vignette('version_control', package = 'git2rdata') for more information.

- New data uses '' as NA string, whereas old data used 'b'.
     Check the 'NA' argument.
--- finished re-building 'plain_text.Rmd'

--- re-building 'split_by.Rmd' using rmarkdown
Quitting from lines 17-121 (split_by.Rmd) 
Error: processing vignette 'split_by.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'split_by.Rmd'

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

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

SUMMARY: processing the following files failed:
  'efficiency.Rmd' 'split_by.Rmd'

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

--- re-building 'package.Rmd' using rmarkdown
Quitting from lines 113-124 (package.Rmd) 
Error: processing vignette 'package.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'package.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'mockery'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'shinyFiles', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', 'mockery'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rtracklayer', 'BSgenome', 'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
Package required but not available: 'Ecdat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GGally', 'dplyr', 'forcats', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'skimr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'tidyr'
Packages suggested but not available for checking: 'testthat', 'lmerTest'
Package unavailable to check Rd xrefs: 'lmerTest'
Packages required but not available:
  'broom', 'broom.mixed', 'dplyr', 'forcats', 'ggplot2', 'rstan',
  'rstantools', 'tibble', 'StanHeaders'

Packages suggested but not available for checking:
  'bayesplot', 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'gghalves', 'ggplot2', 'ggpubr', 'plotly', 'qvalue'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'car', 'dotwhisker', 'broom', 'broom.mixed'
Error(s) in re-building vignettes:
--- re-building 'covstruct.rmd' using rmarkdown
--- finished re-building 'covstruct.rmd'

--- re-building 'mcmc.rmd' using rmarkdown
--- finished re-building 'mcmc.rmd'

--- re-building 'miscEx.rmd' using rmarkdown
--- finished re-building 'miscEx.rmd'

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

--- re-building 'sim.rmd' using rmarkdown
Quitting from lines 19-21 (sim.rmd) 
Error: processing vignette 'sim.rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'sim.rmd'

--- re-building 'troubleshooting.rmd' using rmarkdown
--- finished re-building 'troubleshooting.rmd'

--- re-building 'glmmTMB.Rnw' using knitr
Loading required package: stats4
Quitting from lines 119-125 (glmmTMB.Rnw) 
Error: processing vignette 'glmmTMB.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'glmmTMB.Rnw'

--- re-building 'model_evaluation.Rnw' using knitr
Quitting from lines 112-129 (model_evaluation.Rnw) 
Error: processing vignette 'model_evaluation.Rnw' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'model_evaluation.Rnw'

SUMMARY: processing the following files failed:
  'sim.rmd' 'glmmTMB.Rnw' 'model_evaluation.Rnw'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv(R_TESTS="")  # needed for cluster creation to work
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'logisticPCA', 'testthat'
Package unavailable to check Rd xrefs: 'logisticPCA'
Error(s) in re-building vignettes:
--- re-building 'glmpca.Rmd' using knitr
Quitting from lines 13-15 (glmpca.Rmd) 
Error: processing vignette 'glmpca.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'glmpca.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'AER'

Packages suggested but not available for checking:
  'schlegel', 'ggplot2', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'cplm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'caret'

Packages suggested but not available for checking: 'FactoMineR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fxregime'
Unavailable namespace imported from by a ':::' call: 'fxregime'
  See the note in ?`:::` about the use of this operator.
Package unavailable to check Rd xrefs: 'fxregime'
Packages required but not available: 'ggplot2', 'RcppParallel'

Package suggested but not available for checking: 'qs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mvSLOUCH'
Package unavailable to check Rd xrefs: 'mvSLOUCH'
Running examples in 'GLSME-Ex.R' failed
The error most likely occurred in:

> ### Name: GLSME-package
> ### Title: Generalized Least Squares with Measurement Error
> ### Aliases: GLSME-package
> ### Keywords: generalized least squares regression measurement error
> 
> ### ** Examples
> 
> n<-3 ## number of species
> apetree<-ape::rtree(n)
> ### Define Brownian motion parameters to be able to simulate data under the Brownian motion model.
> BMparameters<-list(vX0=matrix(0,nrow=2,ncol=1),Sxx=rbind(c(1,0),c(0.2,1)))
> ### Now simulate the data and remove the values corresponding to the internal nodes.
> xydata<-mvSLOUCH::simulBMProcPhylTree(apetree,X0=BMparameters$vX0,Sigma=BMparameters$Sxx)
Error in loadNamespace(x) : there is no package called 'mvSLOUCH'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'rvest', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'github-spec.Rmd' using rmarkdown
Quitting from lines 21-24 (github-spec.Rmd) 
Error: processing vignette 'github-spec.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'github-spec.Rmd'

--- re-building 'literal-programming.Rmd' using rmarkdown
Quitting from lines 20-24 (literal-programming.Rmd) 
Error: processing vignette 'literal-programming.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'literal-programming.Rmd'

SUMMARY: processing the following files failed:
  'github-spec.Rmd' 'literal-programming.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'forcats', 'ggplot2', 'dplyr'
Packages required but not available: 'ggplot2', 'tidyr', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gargle', 'rematch2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'Hmisc', 'RcmdrMisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'usage-example-general-model.Rmd' using rmarkdown
--- finished re-building 'usage-example-general-model.Rmd'

--- re-building 'usage-example-special-model.Rmd' using rmarkdown
--- finished re-building 'usage-example-special-model.Rmd'

--- re-building 'usage-shiny-graphical-interface.Rmd' using rmarkdown
--- finished re-building 'usage-shiny-graphical-interface.Rmd'

--- re-building 'GMCM-JStatSoft.Rnw' using knitr
Quitting from lines 128-128 (GMCM-JStatSoft.Rnw) 
Error: processing vignette 'GMCM-JStatSoft.Rnw' failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building 'GMCM-JStatSoft.Rnw'

SUMMARY: processing the following file failed:
  'GMCM-JStatSoft.Rnw'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'Deducer'
Package required but not available: 'SeqVarTools'

Packages suggested but not available for checking: 'doMC', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'gmm_with_R.rnw' using knitr
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Quitting from lines 352-354 (gmm_with_R.rnw) 
Error: processing vignette 'gmm_with_R.rnw' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'gmm_with_R.rnw'

SUMMARY: processing the following file failed:
  'gmm_with_R.rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mlogit'

Packages suggested but not available for checking:
  'AER', 'car', 'memisc', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'rms'
Packages required but not available:
  'ggrepel', 'ggplot2', 'tidyr', 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'roxygen2', 'ggsci', 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'magclass', 'qgraph', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sensitivity'
Package required but not available: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'Hmisc'

Package suggested but not available for checking: 'BiodiversityR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quanteda'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'rhandsontable' 'shiny' 'stats'
  All declared Imports should be used.
Package required but not available: 'WGCNA'

Package suggested but not available for checking: 'WGCNA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'pkgload', 'roxygen2', 'testthat', 'usethis'

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'rcmdcheck', 'pkgbuild'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'car'
Error(s) in re-building vignettes:
--- re-building 'GoodmanKruskal.Rmd' using rmarkdown
Loading required package: GoodmanKruskal
Loading required package: MASS
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'car'
Quitting from lines 148-151 (GoodmanKruskal.Rmd) 
Error: processing vignette 'GoodmanKruskal.Rmd' failed with diagnostics:
object 'Greene' not found
--- failed re-building 'GoodmanKruskal.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'lintr', 'rcmdcheck'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'googleAuthR', 'measurementProtocol', 'tibble',
  'tidyr', 'usethis'

Packages suggested but not available for checking:
  'bigQueryR', 'ganalytics', 'googleCloudStorageR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'gargle'

Packages suggested but not available for checking:
  'bigQueryR', 'devtools', 'googleAnalyticsR', 'roxygen2', 'testthat',
  'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'googleAuthR', 'googleCloudStorageR', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'googleAuthR'

Packages suggested but not available for checking:
  'cli', 'googleComputeEngineR', 'readr', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'googleAuthR'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'googleAuthR'

Packages suggested but not available for checking:
  'googleCloudStorageR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'gargle', 'pillar', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'googleAuthR', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'rvest', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'sfencode.Rmd' using rmarkdown
Quitting from lines 88-95 (sfencode.Rmd) 
Error: processing vignette 'sfencode.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building 'sfencode.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'googleAuthR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cellranger', 'cli', 'gargle', 'googledrive', 'rematch2', 'tibble'

Packages suggested but not available for checking: 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cellranger', 'dplyr', 'readr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'googleAuthR', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'manual_tests.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggdendro'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggraph', 'network', 'dplyr', 'biomaRt', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gms'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gpboost/gpboost.Rcheck/00install.out' for details.
Packages required but not available: 'fields', 'fda', 'fda.usc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'fields', 'testthat'
Running examples in 'GpGp-Ex.R' failed
The error most likely occurred in:

> ### Name: L_mult
> ### Title: Multiply approximate Cholesky by a vector
> ### Aliases: L_mult
> 
> ### ** Examples
> 
> n <- 2000
> locs <- matrix( runif(2*n), n, 2 )
> covparms <- c(2, 0.2, 0.75, 0.1)
> ord <- order_maxmin(locs)
> NNarray <- find_ordered_nn(locs,20)
Error in loadNamespace(x) : there is no package called 'fields'
Calls: find_ordered_nn ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Found the following significant warnings:
  WARNING: failed to apply patch patches/CRAN/gpg.diff
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gpg/gpg.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
This is gplite version 0.12.0
Quitting from lines 37-40 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rstan', 'ggplot2', 'ggthemes'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gptk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly', 'tidyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'nbpMatching'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaflet', 'leaflet.extras', 'plotKML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggthemes'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'usethis'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'ggplot2', 'landscapetools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'cowplot', 'ggthemes', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'hexSticker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'devtools', 'agricolae', 'ggpubr', 'Hmisc', 'ggplot2'

Packages suggested but not available for checking:
  'kableExtra', 'summarytools', 'desplot', 'PairedData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'pegas', 'tidyr', 'sf', 'diveRsity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sparklyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'sf', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qgraph', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggraph', 'ggplot2'
Running examples in 'graphlayouts-Ex.R' failed
The error most likely occurred in:

> ### Name: annotate_circle
> ### Title: annotate concentric circles
> ### Aliases: annotate_circle
> 
> ### ** Examples
> 
> library(igraph)

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

> library(ggraph)
Error in library(ggraph) : there is no package called 'ggraph'
Execution halted
Packages required but not available: 'ggplot2', 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'vdiffr'
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'rtweet', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'dplyr'
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 40-44 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'tibble', 'dplyr', 'tidyr', 'patchwork'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quadmesh'

Packages suggested but not available for checking:
  'devtools', 'oce', 'rworldmap', 'sf', 'spex', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tsfeatures', 'forecast', 'dplyr', 'tibble', 'GA', 'tsibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

Packages suggested but not available for checking:
  'dplyr', 'dtplyr', 'ggplot2', 'ggrepel', 'taxstats', 'taxstats1516',
  'testthat', 'tibble', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tsibble', 'tibble', 'tidyr', 'ggplot2', 'lvplot',
  'ggridges'

Packages suggested but not available for checking:
  'tsibbledata', 'testthat', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr', 'GGally'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'swirlify', 'swirl', 'testthat'
Packages required but not available: 'Gmisc', 'Hmisc', 'rms', 'Epi'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mclust'
  All declared Imports should be used.
Packages required but not available: 'Hmisc', 'rms', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'DiagrammeR', 'bayesplot', 'testthat', 'tidyverse', 'fields'
Package required but not available: 'lamW'

Packages suggested but not available for checking:
  'smooth', 'doMC', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'egg', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'arrangeGrob.rmd' using rmarkdown
Quitting from lines 24-33 (arrangeGrob.rmd) 
Error: processing vignette 'arrangeGrob.rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'arrangeGrob.rmd'

--- re-building 'gtable.Rmd' using rmarkdown
Loading required package: gtable
Loading required package: ggplot2
Quitting from lines 39-48 (gtable.Rmd) 
Error: processing vignette 'gtable.Rmd' failed with diagnostics:
could not find function "ggplotGrob"
--- failed re-building 'gtable.Rmd'

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

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

SUMMARY: processing the following files failed:
  'arrangeGrob.rmd' 'gtable.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'sf'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'vdiffr'
Packages required but not available: 'usethis', 'GA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'msm'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rearrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'ggplot2', 'lmerTest', 'testthat', 'xpectr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qvalue'

Package suggested but not available for checking: 'snplist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'rjags'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'Growthcurver-vignette.Rmd' using rmarkdown
Quitting from lines 312-323 (Growthcurver-vignette.Rmd) 
Error: processing vignette 'Growthcurver-vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'Growthcurver-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dae', 'ggplot2', 'readxl', 'Hmisc', 'GGally'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'missSBM', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'PrimarySchool.Rmd' using rmarkdown
--- finished re-building 'PrimarySchool.Rmd'

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

--- re-building 'les_miserables.Rmd' using rmarkdown
Quitting from lines 18-22 (les_miserables.Rmd) 
Error: processing vignette 'les_miserables.Rmd' failed with diagnostics:
there is no package called 'missSBM'
--- failed re-building 'les_miserables.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'fastDummies', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'msigdbr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'gt', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cellWise', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'gsignal.Rmd' using rmarkdown
Quitting from lines 360-378 (gsignal.Rmd) 
Error: processing vignette 'gsignal.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'gsignal.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'nflfastR'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 64-75 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'roxygen2', 'testthat', 'tidyr'
Packages suggested but not available for checking: 'fields', 'sf', 'stars'
Error(s) in re-building vignettes:
--- re-building 'profiling.Rmd' using rmarkdown
Quitting from lines 22-34 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'profiling.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sf', 'lwgeom', 'readr'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cli'

Packages suggested but not available for checking:
  'alphahull', 'dodgr', 'leafem', 'lwgeom', 'mapview', 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking: 'lwgeom', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'SGP', 'taxize'
Packages unavailable to check Rd xrefs: 'taxize', 'SGP', 'car'
Package required but not available: 'hts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'paletteer', 'testthat', 'rvest', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'broom.helpers', 'cli', 'dplyr', 'forcats', 'gt', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'broom.mixed', 'car', 'geepack', 'GGally', 'Hmisc', 'kableExtra',
  'mice', 'parsnip', 'testthat', 'workflows'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'spdep', 'adespatial', 'car', 'ggplot2', 'ggrepel'
Running examples in 'Guerry-Ex.R' failed
The error most likely occurred in:

> ### Name: Guerry
> ### Title: Data from A.-M. Guerry, "Essay on the Moral Statistics of
> ###   France"
> ### Aliases: Guerry
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'MultiSpat.Rmd' using rmarkdown
Quitting from lines 33-39 (MultiSpat.Rmd) 
Error: processing vignette 'MultiSpat.Rmd' failed with diagnostics:
there is no package called 'spdep'
--- failed re-building 'MultiSpat.Rmd'

--- re-building 'guerry-multivariate.Rmd' using rmarkdown
Quitting from lines 40-45 (guerry-multivariate.Rmd) 
Error: processing vignette 'guerry-multivariate.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'guerry-multivariate.Rmd'

SUMMARY: processing the following files failed:
  'MultiSpat.Rmd' 'guerry-multivariate.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'tibble', 'dplyr'
Packages required but not available: 'dplyr', 'readr'

Packages suggested but not available for checking:
  'testthat', 'tidytext', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'drc'
Package required but not available: 'tsDyn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'eda4treeR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ergm', 'ggplot2', 'dplyr', 'network', 'sna', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spdep', 'GWmodel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'run-tests.R'
Running the tests in 'tests/run-tests.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'spgwr'
  All declared Imports should be used.
Packages required but not available: 'spatialreg', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'golem', 'sf', 'dplyr', 'plotly', 'viridis', 'leaflet', 'pkgload'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'broom', 'plotROC', 'kableExtra', 'ggrepel',
  'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'IRdisplay', 'plotly', 'repr'
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'gapminder', 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'readxl', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'rhdf5', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr', 'tidyr'
Packages suggested but not available for checking:
  'nbpMatching', 'lmerTest'
Packages suggested but not available for checking:
  'devtools', 'pkgload', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'A_Haplin_intro_installation.Rmd' using rmarkdown
--- finished re-building 'A_Haplin_intro_installation.Rmd'

--- re-building 'B_Reading_data.Rmd' using rmarkdown
Read 6 items
Read 1494 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
Read 6 items
Read 1494 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
--- finished re-building 'B_Reading_data.Rmd'

--- re-building 'C_Running_Haplin.Rmd' using rmarkdown
Read 6 items
Read 1494 items
Read 0 items
Read 8 items
Read 9112 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
Quitting from lines 150-151 (C_Running_Haplin.Rmd) 
Error: processing vignette 'C_Running_Haplin.Rmd' failed with diagnostics:
ggplot2 cannot be loaded!
--- failed re-building 'C_Running_Haplin.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'rms'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'gh', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'devtools', 'recipes', 'roxygen2', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'harmonicmeanp.Rmd' using rmarkdown
Quitting from lines 389-402 (harmonicmeanp.Rmd) 
Error: processing vignette 'harmonicmeanp.Rmd' failed with diagnostics:
need finite 'xlim' values
--- failed re-building 'harmonicmeanp.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'cowplot', 'tidyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking: 'Seurat', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggtree', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'accessors.R'
Running the tests in 'tests/accessors.R' failed.
Complete output:
  > library(hash)
  hash-2.2.6.1 provided by Decision Patterns
  
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'forcats', 'readr', 'tibble'

Packages suggested but not available for checking:
  'cli', 'pillar', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'hazus_demo.Rmd' using knitr
Quitting from lines 34-37 (hazus_demo.Rmd) 
Error: processing vignette 'hazus_demo.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'hazus_demo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rstan', 'ggplot2', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_check("hbbr")
  Error in test_check("hbbr") : could not find function "test_check"
  Execution halted
Package required but not available: 'dendextend'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dplyr', 'colourpicker'
Running examples in 'hchinamap-Ex.R' failed
The error most likely occurred in:

> ### Name: hchinamap
> ### Title: 'hchinamap': Mapping China and Its Provinces, Municipalities and
> ###   Autonomous Regions using R and 'Highmaps'
> ### Aliases: hchinamap
> 
> ### ** Examples
> 
> library(hchinamap)
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'hchinamap.Rmd' using rmarkdown
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'hchinamap.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'klaR'
Packages required but not available: 'readxl', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'leaflet', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'nycflights13'
Found the following significant warnings:
  H5ls.c:78:73: warning: too many arguments for format [-Wformat-extra-args]
  H5ls.c:88:84: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hdf5r/hdf5r.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'hdf5r.Rmd' using rmarkdown
Quitting from lines 86-92 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
there is no package called 'nycflights13'
--- failed re-building 'hdf5r.Rmd'

SUMMARY: processing the following file failed:
  'hdf5r.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'Directional'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'Hmisc', 'questionr', 'tidyverse', 'tibble', 'ggjoy',
  'ggplot2', 'tidyr', 'ggridges', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'EstimDiagnostics', 'waldo'
Running examples in 'HDShOP-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_frontier
> ### Title: Plot the Bayesian efficient frontier (Bauder et al. 2021) and
> ###   the provided portfolios.
> ### Aliases: plot_frontier
> 
> ### ** Examples
> 
> p = 150
> n = 300
> gamma <- 10
> mu = seq(0.2,-0.2, length.out=p)
> Sigma = RandCovMtrx(p=p)
> 
> x <- t(MASS::mvrnorm(n=n , mu=mu, Sigma=Sigma))
> 
> EW_port <- rep(1/p, length=p)
> MV_shr_port <- new_MV_portfolio_weights_BDOPS21(x=x, gamma=gamma, b=EW_port, beta=0.05)$weights
> GMV_shr_port <- new_MV_portfolio_weights_BDOPS21(x=x, gamma=Inf, b=EW_port, beta=0.05)$weights
> MV_trad_port <- new_MV_portfolio_traditional(x=x, gamma=gamma)$weights
> GMV_trad_port <- new_MV_portfolio_traditional(x=x, gamma=Inf)$weights
> 
> weights.eff = cbind(EW_port, MV_shr_port, GMV_shr_port, MV_trad_port, GMV_trad_port)
> colnames(weights.eff) <- c("EW", "MV_shr", "GMV_shr", "MV_trad", "GMV_trad")
> 
> 
> Fplot <- plot_frontier(x, weights.eff)
         portfolio.return portfolio.sd    names
EW            0.005207494   0.13595588       EW
MV_shr        0.232142340   0.12826610   MV_shr
GMV_shr       0.011918657   0.04836688  GMV_shr
MV_trad       0.893648342   0.29960052  MV_trad
GMV_trad      0.013479146   0.04175584 GMV_trad
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: plot_frontier ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'swfscMisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'cowplot', 'dplyr', 'ggplot2', 'recipes', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'lintr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'timetk', 'ggplot2', 'dplyr', 'cowplot', 'tidyr', 'ggrepel'

Packages suggested but not available for checking:
  'roxygen2', 'broom', 'tidyquant'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'timetk', 'dplyr', 'ggplot2', 'tidyquant', 'plotly',
  'recipes'

Packages suggested but not available for checking: 'roxygen2', 'rsample'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'healthyR', 'healthyR.ts', 'dplyr', 'tibble', 'cli'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotly', 'viridis', 'ggplot2', 'dendextend', 'egg'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'ggpubr', 'rerddap', 'testthat', 'tidync', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sampleSelection'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'dplyr', 'tidyr', 'nycflights13', 'ggplot2'
Packages unavailable to check Rd xrefs: 'dplyr', 'tidyr', 'tibble'
Running examples in 'heddlr-Ex.R' failed
The error most likely occurred in:

> ### Name: make_template
> ### Title: Linearly combine template elements into templates
> ### Aliases: make_template
> 
> ### ** Examples
> 
> 
> # When passed vectors, make_template flattens each vector into a single
> # string and then combines its arguments from left to right
> spList <- data.frame(Species = c(unique(iris$Species), "test string"))
> make_template(
+   heddle(spList, "SPECIES CODE GWAR ", "GWAR" = Species),
+   heddle(spList, "SPECIES CODE GWAR ", "GWAR" = Species)
+ )
[1] "SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string "
> 
> # When passed variables in a dataframe, make_template collapses each column
> # in turn, then combines the output strings from left to right
> spList <- data.frame(Species = c(unique(iris$Species), "test string"))
> spList$template <- heddle(spList, "SPECIES CODE GWAR ", "GWAR" = Species)
> make_template(spList, template)
[1] "SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string "
> make_template(spList, template, template)
[1] "SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string "
> 
> # When passed nested columns, heddlr collapses each cell into a string,
> # then collapses each column into a string, and then combines the outputs
> # from left to right
> make_template(tidyr::nest(spList, nested = template), nested)
Error in loadNamespace(x) : there is no package called 'tidyr'
Calls: make_template ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'modular-reporting-with-heddlr.Rmd' using rmarkdown
Quitting from lines 188-191 (modular-reporting-with-heddlr.Rmd) 
Error: processing vignette 'modular-reporting-with-heddlr.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'modular-reporting-with-heddlr.Rmd'

SUMMARY: processing the following file failed:
  'modular-reporting-with-heddlr.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'BCEA', 'flexsurv', 'readxl', 'rgho', 'testthat', 'cli'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggforce'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'taxize'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sf'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'precrec'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

Packages suggested but not available for checking: 'candisc', 'mvinfluence'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'flexpolyline', 'sf'

Packages suggested but not available for checking:
  'ggplot2', 'leafpop', 'lwgeom', 'mapview', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cplm', 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'patchwork'
Error(s) in re-building vignettes:
--- re-building 'hermiter.Rmd' using rmarkdown
Quitting from lines 63-70 (hermiter.Rmd) 
Error: processing vignette 'hermiter.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'hermiter.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'fields'

Packages suggested but not available for checking:
  'autoimage', 'devtools', 'fda', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'flexsurv', 'ggplot2'

Packages suggested but not available for checking:
  'kableExtra', 'mstate', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'Matrix'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'tidyverse'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bupaR', 'processmapR', 'dplyr', 'tidyr', 'DiagrammeR', 'petrinetR',
  'ggplot2', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggimage', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DiagrammeR', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'rmarkdown'
  All declared Imports should be used.
Package required but not available: 'Hmisc'

Packages suggested but not available for checking:
  'car', 'Rcmdr', 'RcmdrPlugin.HH', 'microplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EMD', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rtracklayer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggdendro', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GGally', 'adegenet', 'diveRsity', 'entropart', 'mmod', 'ggplot2',
  'hierfstat', 'tibble', 'pegas'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adegenet', 'gaston'

Packages suggested but not available for checking: 'pegas', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'broom', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'gapminder', 'forecast', 'geojsonio', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'cubature' 'mvtnorm'
  All declared Imports should be used.
Running examples in 'highlightHTML-Ex.R' failed
The error most likely occurred in:

> ### Name: table_id_inject
> ### Title: Table hash addition for markup
> ### Aliases: table_id_inject
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'the_basics.Rmd' using rmarkdown
Quitting from lines 118-132 (the_basics.Rmd) 
Error: processing vignette 'the_basics.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'the_basics.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'comparing_samples.Rmd' using rmarkdown
Quitting from lines 78-86 (comparing_samples.Rmd) 
Error: processing vignette 'comparing_samples.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'comparing_samples.Rmd'

--- re-building 'identifying_effects.Rmd' using rmarkdown
Warning in make.cut(fullMat, n = nbins + 1, count.lim = 40) :
  n is much larger than the suggested number of cuts: 2 see ?hilbert.order
Quitting from lines 131-151 (identifying_effects.Rmd) 
Error: processing vignette 'identifying_effects.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'identifying_effects.Rmd'

SUMMARY: processing the following files failed:
  'comparing_samples.Rmd' 'identifying_effects.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'ggpubr', 'qgraph', 'FSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cppRouting', 'dplyr', 'ggplot2', 'lwgeom', 'sf', 'tidyr'

Packages suggested but not available for checking:
  'airportr', 'cowplot', 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rms'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'car', 'heplots'
Package unavailable to check Rd xrefs: 'alr4'
Running examples in 'HistData-Ex.R' failed
The error most likely occurred in:

> ### Name: CushnyPeebles
> ### Title: Cushny-Peebles Data: Soporific Effects of Scopolamine
> ###   Derivatives
> ### Aliases: CushnyPeebles CushnyPeeblesN
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(CushnyPeebles)
> # quick looks at the data
> plot(CushnyPeebles)
> boxplot(CushnyPeebles, ylab="Hours of Sleep", xlab="Treatment")
> 
> ##########################
> # Repeated measures MANOVA
> 
> CPmod <- lm(cbind(Control, L_hyoscyamine, L_hyoscine, DL_hyoscine) ~ 1, data=CushnyPeebles)
> 
> # Assign within-S factor and contrasts
> Treatment <- factor(colnames(CushnyPeebles), levels=colnames(CushnyPeebles))
> contrasts(Treatment) <- matrix(
+ 	c(-3, 1, 1, 1,
+ 	   0,-2, 1, 1,
+ 	   0, 0,-1, 1), ncol=3)
> colnames(contrasts(Treatment)) <- c("Control.Drug", "L.DL", "L_hy.DL_hy")
> 
> Treats <- data.frame(Treatment)
> if (require(car)) {
+ (CPaov <- Anova(CPmod, idata=Treats, idesign= ~Treatment))
+ }
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'car'
> summary(CPaov, univariate=FALSE)
Error in summary(CPaov, univariate = FALSE) : object 'CPaov' not found
Execution halted
Packages required but not available: 'FactoMineR', 'ggplot2', 'ggridges'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'trackr'
Packages suggested but not available for checking: 'sna', 'bipartite'
Running examples in 'HiveR-Ex.R' failed
The error most likely occurred in:

> ### Name: adj2HPD
> ### Title: Process an Adjacency Graph into a HivePlotData Object
> ### Aliases: adj2HPD
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> ### Example 1: a bipartite network
> ### Note: this first example has questionable scientific value!
> ### The purpose is to show how to troubleshoot and
> ### manipulate a HivePlotData object.
> 
> require(bipartite)
Loading required package: bipartite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'bipartite'
> data(Safariland) # This is a bipartite network
Warning in data(Safariland) : data set 'Safariland' not found
> 
> # You may wish to do ?Safariland or ?Safari for background
> 
> hive1 <- adj2HPD(Safariland, desc = "Safariland data set from bipartite")
Error in adj2HPD(Safariland, desc = "Safariland data set from bipartite") : 
  object 'Safariland' not found
Execution halted
Error(s) in re-building vignettes:
--- re-building 'HiveR.Rmd' using rmarkdown
Quitting from lines 24-41 (HiveR.Rmd) 
Error: processing vignette 'HiveR.Rmd' failed with diagnostics:
there is no package called 'sna'
--- failed re-building 'HiveR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'ggpubr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dplyr', 'tidyr'
Packages required but not available:
  'devtools', 'usethis', 'tidyverse', 'dplyr', 'tibble', 'tidyr',
  'readr', 'readxlsb'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'janitor', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'car', 'qqplotr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Rcpp' 'methods' 'rgl'
  All declared Imports should be used.
Packages required but not available: 'broom.mixed', 'mice'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'viridis'

Packages suggested but not available for checking: 'rms', 'mice', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'HMP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rsamtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'readr', 'dplyr', 'tidyr', 'patchwork', 'rvest', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'mice', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'endtoend'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'usethis', 'roxygen2'
Packages suggested but not available for checking: 'Hmisc', 'ggplot2'
Running examples in 'horseshoe-Ex.R' failed
The error most likely occurred in:

> ### Name: HS.normal.means
> ### Title: The horseshoe prior for the sparse normal means problem
> ### Aliases: HS.normal.means
> 
> ### ** Examples
> 
> #Empirical Bayes example with 20 signals, rest is noise
> #Posterior mean for the signals is plotted
> #And variable selection is performed using the credible intervals
> #And the credible intervals are plotted
> truth <- c(rep(0, 80), rep(8, 20))
> data <-  truth + rnorm(100, 1)
> tau.hat <- HS.MMLE(data, Sigma2 = 1)
> res.HS1 <- HS.normal.means(data, method.tau = "fixed", tau = tau.hat,
+ method.sigma = "fixed", Sigma2 = 1)
[1] 1000
[1] 2000
[1] 3000
[1] 4000
[1] 5000
[1] 6000
> #Plot the posterior mean against the data (signals in blue)
> plot(data, res.HS1$BetaHat, col = c(rep("black", 80), rep("blue", 20)))
> #Find the selected betas (ideally, the last 20 are equal to 1)
> HS.var.select(res.HS1, data, method = "intervals")
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
 [75] 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> #Plot the credible intervals
> library(Hmisc)
Error in library(Hmisc) : there is no package called 'Hmisc'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'horseshoe-vignette.Rmd' using rmarkdown
Quitting from lines 13-18 (horseshoe-vignette.Rmd) 
Error: processing vignette 'horseshoe-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'horseshoe-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mice'

Package suggested but not available for checking: 'miceadds'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'FactoMineR', 'ggforce', 'ggplot2', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'colourpicker'
Package required but not available: 'RcppParallel'

Packages suggested but not available for checking:
  'ggplot2', 'sampleSelection', 'GA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'imputeTS', 'forecast', 'pdp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RISCA'
Packages required but not available: 'ggplot2', 'doBy', 'pseudorank'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spdep', 'spatialreg'

Packages suggested but not available for checking: 'sf', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'npregfast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggpubr', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rstan', 'rstantools', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'bayesplot'
Running examples in 'HTLR-Ex.R' failed
The error most likely occurred in:

> ### Name: gendata_FAM
> ### Title: Generate Simulated Data with Factor Analysis Model
> ### Aliases: gendata_FAM
> 
> ### ** Examples
> 
> ## feature #1: marginally related feature
> ## feature #2: marginally unrelated feature, but feature #2 is correlated with feature #1
> ## feature #3-5: marginally related features and also internally correlated
> ## feature #6-10: noise features without relationship with the y
> 
> set.seed(12345)
> n <- 100
> p <- 10
> 
> means <- rbind(
+   c(0, 1, 0),
+   c(0, 0, 0),
+   c(0, 0, 1),
+   c(0, 0, 1),
+   c(0, 0, 1)
+ ) * 2
> 
> means <- rbind(means, matrix(0, p - 5, 3))
> 
> A <- diag(1, p)
> A[1:5, 1:3] <- rbind(
+   c(1, 0, 0),
+   c(2, 1, 0),
+   c(0, 0, 1),
+   c(0, 0, 1),
+   c(0, 0, 1)
+ )
> 
> dat <- gendata_FAM(n, means, A, sd_g = 0.5, stdx = TRUE)
> ggplot2::qplot(dat$y, bins = 6)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'dplyr', 'rvest', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'Hmisc', 'tibble', 'tidyr', 'dplyr'
Packages unavailable to check Rd xrefs: 'Hmisc', 'tibble', 'tidyr', 'dplyr'
Running examples in 'htmlTable-Ex.R' failed
The error most likely occurred in:

> ### Name: tidyHtmlTable
> ### Title: Generate an htmlTable using tidy data as input
> ### Aliases: tidyHtmlTable
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called 'tibble'
Execution halted
Running 'testInteractive.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'complex_tables.Rmd' using rmarkdown
Quitting from lines 120-160 (complex_tables.Rmd) 
Error: processing vignette 'complex_tables.Rmd' failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building 'complex_tables.Rmd'

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

--- re-building 'tidyHtmlTable.Rmd' using rmarkdown
Quitting from lines 29-39 (tidyHtmlTable.Rmd) 
Error: processing vignette 'tidyHtmlTable.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'tidyHtmlTable.Rmd'

SUMMARY: processing the following files failed:
  'complex_tables.Rmd' 'tidyHtmlTable.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'htmltab.Rmd' using rmarkdown
Quitting from lines 47-50 (htmltab.Rmd) 
Error: processing vignette 'htmltab.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'htmltab.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'rvest'
Package suggested but not available for checking: 'HTSFilter'
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'readr', 'readxl', 'openair',
  'editData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'DESeq2', 'phyloseq'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'GGally', 'EnvStats', 'viridis', 'cowplot', 'ggrepel',
  'dplyr', 'forcats', 'testthat'
Package suggested but not available for checking: 'httptest'
Error(s) in re-building vignettes:
--- re-building 'httpcache.Rmd' using rmarkdown
Quitting from lines 91-92 (httpcache.Rmd) 
Error: processing vignette 'httpcache.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'httpcache.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'testthat'

Package suggested but not available for checking: 'pkgload'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'humidity-measures.Rmd' using rmarkdown
--- finished re-building 'humidity-measures.Rmd'

--- re-building 'ivt_ivs-sh.Rmd' using rmarkdown
Quitting from lines 33-45 (ivt_ivs-sh.Rmd) 
Error: processing vignette 'ivt_ivs-sh.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'ivt_ivs-sh.Rmd'

SUMMARY: processing the following file failed:
  'ivt_ivs-sh.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggmap', 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'hurricaneexposuredata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'bench', 'testthat'
Package unavailable to check Rd xrefs: 'bench'
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'Hmisc', 'nycflights13', 'ggplot2', 'readr',
  'tibble', 'tidyr'
Packages suggested but not available for checking:
  'AER', 'broom', 'broom.mixed', 'devtools', 'dplyr', 'ftExtra',
  'ggplot2', 'testthat', 'tibble'
Namespaces in Imports field not imported from:
  'R6' 'xml2'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'dplyr', 'tibble'
Running examples in 'huxtable-Ex.R' failed
The error most likely occurred in:

> ### Name: by_cases
> ### Title: Map cell contents to properties using 'case_when'
> ### Aliases: by_cases
> 
> ### ** Examples
> 
> if (! requireNamespace("dplyr")) {
+   stop("Please install the 'dplyr' package to run this example")
+ }
Loading required namespace: dplyr
Failed with error:  'there is no package called 'dplyr''
Error: Please install the 'dplyr' package to run this example
Execution halted
Error(s) in re-building vignettes:
--- re-building 'design-principles.Rmd' using rmarkdown
--- finished re-building 'design-principles.Rmd'

--- re-building 'huxreg.Rmd' using rmarkdown
Quitting from lines 44-50 (huxreg.Rmd) 
Error: processing vignette 'huxreg.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'huxreg.Rmd'

--- re-building 'huxtable.Rmd' using rmarkdown
Quitting from lines 21-41 (huxtable.Rmd) 
Error: processing vignette 'huxtable.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'huxtable.Rmd'

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

SUMMARY: processing the following files failed:
  'huxreg.Rmd' 'huxtable.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'colourpicker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DiagrammeR', 'dplyr', 'pixiedust'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'readr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'hydrostats-Ex.R' failed
The error most likely occurred in:

> ### Name: flood.length.max
> ### Title: Calculates the maximum flood length in a time series.
> ### Aliases: flood.length.max
> 
> ### ** Examples
> 
> 
> data(Cooper)
> Cooper<-ts.format(Cooper)
> 
> flood.length.max(Cooper, threshold = 50000, ind.days = 5)
  max.duration
1           40
> 
> # Return annual maximum flood length based on calendar year using ddply (from plyr package) 
> require(plyr)
Loading required package: plyr
> Cooper$Year=format(Cooper$Date, format="%Y")
> ddply(Cooper, .(Year), flood.length.max, threshold = 50000)
   Year max.duration
1  1967            0
2  1968           13
3  1969            0
4  1970            0
5  1971           10
6  1972            6
7  1973           17
8  1974           40
9  1975            2
10 1976           21
11 1977           19
12 1978            0
13 1979            8
14 1980            1
15 1981            3
16 1982            0
17 1983           10
18 1984            0
19 1985            0
20 1986            7
21 1987            0
> 
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'
> Cooper %>%
+ dplyr::group_by(Year) %>%
+ dplyr::do(flood.length.max(., threshold = 50000))
Error in Cooper %>% dplyr::group_by(Year) %>% dplyr::do(flood.length.max(.,  : 
  could not find function "%>%"
Execution halted
Packages required but not available: 'ggplot2', 'plotly', 'readxl'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'flowCore'
Packages suggested but not available for checking: 'testthat', 'jack'
Packages required but not available: 'matlib', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'unbalanced'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'testthat', 'dplyr'

Packages suggested but not available for checking: 'devtools', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dplyr', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'Getting_started_with_the_R_package_hystReet.Rmd' using rmarkdown

Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 34-39 (Getting_started_with_the_R_package_hystReet.Rmd) 
Error: processing vignette 'Getting_started_with_the_R_package_hystReet.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Getting_started_with_the_R_package_hystReet.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ymlthis'

Packages suggested but not available for checking:
  'plotly', 'testthat', 'ggplot2', 'gt', 'kableExtra', 'forcats',
  'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'incidence2', 'trending', 'dplyr', 'tibble', 'tidyr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'a_intro.Rmd' using rmarkdown
--- finished re-building 'a_intro.Rmd'

--- re-building 'b_analysis.Rmd' using rmarkdown
Quitting from lines 37-40 (b_analysis.Rmd) 
Error: processing vignette 'b_analysis.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'b_analysis.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dslabs', 'ggplot2', 'dplyr', 'Ecdat', 'kableExtra'

Packages suggested but not available for checking:
  'tidyverse', 'caret', 'ggrepel', 'cowplot', 'gutenbergr', 'tidytext',
  'rvest', 'Lahman', 'waldo', 'usethis', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'SparkR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tidyr', 'dplyr', 'ggplot2'

Package suggested but not available for checking: 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'DALEX', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BSgenome', 'dplyr'

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'icd'
Packages suggested but not available for checking: 'fields', 'viridis'
Namespace in Imports field not imported from: 'coda'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'FitAndGenerateContours.Rmd' using rmarkdown
Loading required package: rgeos
Loading required package: sp
rgeos version: 0.5-5, (SVN revision 640)
 GEOS runtime version: 3.6.2-CAPI-1.10.2 
 Linking to sp version: 1.4-5 
 Polygon checking: TRUE 

Loading required package: maptools
Checking rgeos availability: TRUE
Quitting from lines 41-44 (FitAndGenerateContours.Rmd) 
Error: processing vignette 'FitAndGenerateContours.Rmd' failed with diagnostics:
there is no package called 'viridis'
--- failed re-building 'FitAndGenerateContours.Rmd'

--- re-building 'MixtureContourForecasts.Rmd' using rmarkdown
Quitting from lines 64-66 (MixtureContourForecasts.Rmd) 
Error: processing vignette 'MixtureContourForecasts.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building 'MixtureContourForecasts.Rmd'

--- re-building 'biasCorrectDemo.Rmd' using rmarkdown
Quitting from lines 60-62 (biasCorrectDemo.Rmd) 
Error: processing vignette 'biasCorrectDemo.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building 'biasCorrectDemo.Rmd'

SUMMARY: processing the following files failed:
  'FitAndGenerateContours.Rmd' 'MixtureContourForecasts.Rmd'
  'biasCorrectDemo.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'plotly', 'ggrepel', 'ggpubr', 'ggdendro', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'frailtypack', 'MIICD', 'dynsurv'
Package required but not available: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'httptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'coefplot', 'forecast', 'openair', 'papeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'kableExtra', 'dendextend'
Error(s) in re-building vignettes:
--- re-building 'index.Rmd' using rmarkdown
Quitting from lines 26-47 (index.Rmd) 
Error: processing vignette 'index.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'index.Rmd'

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

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

> ### Name: survplot
> ### Title: 'Plotting individual survival curves'
> ### Aliases: survplot
> 
> ### ** Examples
> 
> # rats data example.
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> data(rat2)
> ## Don't show: 
>  set.seed(1)
>  rats.icrf <-
+    icrf(~ dose.lvl + weight + male + cage.no, data = rat2,
+         data.type = "currentstatus", currentstatus.label = c("survtime", "tumor"),
+         returnBest = TRUE, ntree=2, nfold=2)

Forest loop 1 out of 2 folds
Tree 1 2 
   IMSE1 (OOB, non-OOB) = (0.131, 0.085), IMSE2 = (0.252, 0.193)
Forest loop 2 out of 2 folds
Tree 1 2 
   IMSE1 (OOB, non-OOB) = (0.134, 0.079), IMSE2 = (0.268, 0.193)
>  survplot(rats.icrf, c(1,3,5))
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: survplot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running examples in 'icr-Ex.R' failed
The error most likely occurred in:

> ### Name: krippalpha
> ### Title: Krippendorff's alpha
> ### Aliases: krippalpha
> 
> ### ** Examples
> 
> data(codings)
> 
> # compute alpha, without uncertainty estimates
> krippalpha(codings)

 Krippendorff's alpha 

 alpha coders units   level
 0.743      4    12 nominal

 Bootstrapped alpha
 Alpha Std. Error 2.5 % 97.5 % Boot. technique Bootstraps
    NA         NA    NA     NA    Krippendorff         NA
    NA         NA    NA     NA   nonparametric         NA

 P(alpha > alpha_min):
 alpha_min krippendorff nonparametric
      0.90           NA            NA
      0.80           NA            NA
      0.70           NA            NA
      0.67           NA            NA
      0.60           NA            NA
      0.50           NA            NA
> 
> # additionally compute bootstrapped uncertainty estimates for alpha
> alpha <- krippalpha(codings, metric = "nominal", bootstrap = TRUE, bootnp = TRUE)
> alpha

 Krippendorff's alpha 

 alpha coders units   level
 0.743      4    12 nominal

 Bootstrapped alpha
 Alpha Std. Error 2.5 % 97.5 % Boot. technique Bootstraps
  0.72      0.074 0.562   0.85    Krippendorff      20000
  0.73      0.146 0.417   1.00   nonparametric       1000

 P(alpha > alpha_min):
 alpha_min krippendorff nonparametric
      0.90        0.004         0.126
      0.80        0.133         0.350
      0.70        0.640         0.607
      0.67        0.739         0.683
      0.60        0.940         0.822
      0.50        0.996         0.932
> 
> # plot bootstrapped alphas
> plot(alpha)
> 
> # alternatively, use ggplot2
> df <- plot(alpha, return_data = TRUE)
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  'ggnewscale', 'ggplot2', 'metR', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'Using_ICvectorfields.Rmd' using rmarkdown
Quitting from lines 19-25 (Using_ICvectorfields.Rmd) 
Error: processing vignette 'Using_ICvectorfields.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Using_ICvectorfields.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'sf'

Packages suggested but not available for checking: 'tidyr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'mlogit'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'mice', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'FRK'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'ggpubr', 'ggtree', 'treeio', 'kableExtra', 'badger'

VignetteBuilder packages required for checking but not installed:
  'kableExtra', 'badger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'viridis', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GD', 'ggplot2', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mzR', 'readxl', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ie2misc', 'ie2miscdata', 'rvest', 'qdap'
Packages suggested but not available for checking: 'ie2misc', 'optiRum'
Namespace in Imports field not imported from: 'testit'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'expm' 'rlecuyer'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'OpenMx'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

Packages suggested but not available for checking:
  'forecast', 'tibble', 'timetk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'patchwork', 'tibble', 'tidyr',
  'plotly'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'igoR.Rmd' using rmarkdown
Quitting from lines 76-82 (igoR.Rmd) 
Error: processing vignette 'igoR.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'igoR.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'reticulate'
  All declared Imports should be used.
Package required but not available: 'ggdendro'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'roxygen2', 'ggplot2', 'readr', 'tibble', 'tidytext'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readxl', 'rvest', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'dplyr', 'readr'

Packages suggested but not available for checking:
  'mockery', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'demography', 'rainbow', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/image.dlib/image.dlib.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'mockery'
Running examples in 'imager-Ex.R' failed
The error most likely occurred in:

> ### Name: as.cimg.data.frame
> ### Title: Create an image from a data.frame
> ### Aliases: as.cimg.data.frame
> 
> ### ** Examples
> 
> #Create a data.frame with columns x,y and value
> df <- expand.grid(x=1:10,y=1:10) %>% dplyr::mutate(value=x*y)
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'gettingstarted.Rmd' using rmarkdown
Loading required package: magrittr

Attaching package: 'imager'

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

    add

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

    convolve, spectrum

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

    frame

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

    save.image

Quitting from lines 152-158 (gettingstarted.Rmd) 
Error: processing vignette 'gettingstarted.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'gettingstarted.Rmd'

--- re-building 'pixsets.Rmd' using rmarkdown
Quitting from lines 107-108 (pixsets.Rmd) 
Error: processing vignette 'pixsets.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'pixsets.Rmd'

SUMMARY: processing the following files failed:
  'gettingstarted.Rmd' 'pixsets.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'jpeg'
  All declared Imports should be used.
Packages required but not available: 'IsingSampler', 'qgraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'MBESS'

Package suggested but not available for checking: 'mediation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'usethis', 'pillar', 'rtweet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'bench', 'caret', 'mlr', 'patchwork', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'proxyC', 'clusterProfiler', 'ggplot2', 'corrr', 'GSVA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'dtplyr', 'patchwork', 'factoextra', 'UpSetR',
  'ggrepel', 'readr', 'readxl', 'airr', 'ggseqlogo', 'ggalluvial',
  'tibble', 'ggpubr', 'dbplyr'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'parallelDist'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lvmisc', 'pillar', 'tibble', 'toOrdinal', 'vroom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dbplyr'

Packages suggested but not available for checking:
  'Lahman', 'nycflights13', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'importar-Ex.R' failed
The error most likely occurred in:

> ### Name: import
> ### Title: This function imports/loads packages as in 'Python', i.e.,
> ###   "import package as alias"
> ### Aliases: import
> 
> ### ** Examples
> 
> import(dplyr, d)
Error in library(package., character.only = TRUE) : 
  there is no package called 'dplyr'
Calls: import -> <Anonymous> -> withCallingHandlers -> library
Execution halted
Packages required but not available: 'Hmisc', 'readxl', 'haven'

Package suggested but not available for checking: 'compareGroups'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'haven'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (C) 2018  Paul Fink
  > #
  > # This file is part of imptree.
  > #
  > # imptree is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 2 of the License, or
  > # (at your option) any later version.
  > #
  > # imptree is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with imptree.  If not, see <https://www.gnu.org/licenses/>.
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'count_compare'
Package required but not available: 'PSF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forecast', 'ggplot2', 'imputeTS', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggtext', 'forecast'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'tsibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'lme4' 'reshape2'
  All declared Imports should be used.
Running examples in 'incase-Ex.R' failed
The error most likely occurred in:

> ### Name: if_case
> ### Title: Pipe-friendly vectorized if
> ### Aliases: if_case
> 
> ### ** Examples
> 
> x <- c(1, 2, 5, NA)
> 
> # if_case() produces the same output as dplyr::if_else()
> if_case(x > 3, "high", "low", "missing")
[1] "low"     "low"     "high"    "missing"
> dplyr::if_else(x > 3, "high", "low", "missing")
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'RcppParallel', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'dtwclust', 'parallelDist', 'dendextend'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'pillar', 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'gfonts'

Packages suggested but not available for checking: 'rcmdcheck', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'testthat'

Packages suggested but not available for checking:
  'ggplot2', 'mockery', 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'SixSigma'

Packages suggested but not available for checking:
  'tibble', 'janitor', 'patchwork', 'forcats', 'broom', 'viridis',
  'car', 'qicharts2', 'ggforce', 'ggraph', 'tidygraph', 'agricolae',
  'RcmdrMisc', 'gt', 'skimr', 'ggtext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibbletime'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'broom', 'devtools', 'nycflights13', 'testthat', 'tidyr', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'tidyr', 'ggplot2', 'UpSetR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'janitor', 'ggplot2'

Packages suggested but not available for checking:
  'Hmisc', 'NNS', 'colourpicker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'httptest'
Package required but not available: 'relevent'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Package suggested but not available for checking: 'rNOMADS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library (testthat);
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'ggmap', 'ggpolypath', 'INLA', 'patchwork', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dataRetrieval', 'inlmisc'
Namespaces in Imports field not imported from:
  'raster' 'sp'
  All declared Imports should be used.
Running examples in 'inldata-Ex.R' failed
The error most likely occurred in:

> ### Name: cities
> ### Title: Cities and Towns
> ### Aliases: cities
> ### Keywords: datasets
> 
> ### ** Examples
> 
> inlmisc::PlotMap(cities, dms.tick = TRUE)
Error in loadNamespace(x) : there is no package called 'inlmisc'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'GA', 'leaflet'

Packages suggested but not available for checking:
  'alphahull', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'nycflights13'
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 235-249 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'nycflights13'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'entropart'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'readr'
Running examples in 'INQC-Ex.R' failed
The error most likely occurred in:

> ### Name: climdex2ecad
> ### Title: Converter from the ClimDex format into the ECA&D format (blended
> ###   version)
> ### Aliases: climdex2ecad
> 
> ### ** Examples
> 
> #Set a temporal working directory:
> wd <- tempdir(); wd0 <- setwd(wd)
> #Create subdirectory where raw data files in the ClimDex format have to be located
> dir.create(file.path(wd, "raw_ClimDex"))
> #Extract the ClimDex data and station files from the example data folder
> path2stalist<-system.file("extdata", "stations.csv", package = "INQC")
> stalist<-readr::read_lines_raw(path2stalist)
Error in loadNamespace(x) : there is no package called 'readr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'broom', 'dplyr', 'ggbeeswarm', 'ggplot2', 'ggpubr', 'ggthemes',
  'patchwork', 'readxl', 'tidyr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'tidyverse', 'kableExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'AER', 'afex', 'BGGM', 'blavaan', 'brms', 'cplm', 'dplyr', 'feisr',
  'geepack', 'gmnl', 'gt', 'ivreg', 'logistf', 'merTools', 'metaBMA',
  'mice', 'mlogit', 'panelr', 'parsnip', 'rms', 'robustlmm',
  'rstanarm', 'rstantools', 'testthat'
Packages required but not available: 'ggplot2', 'InterVA5'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfittext', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'pkgbuild', 'testthat', 'mockery'
Packages required but not available:
  'ciTools', 'dplyr', 'ggplot2', 'patchwork', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'DiagrammeR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'diffeR', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenomicAlignments', 'biomaRt', 'Rsamtools', 'rPref', 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'cli', 'jtools', 'tibble'

Packages suggested but not available for checking:
  'broom', 'cowplot', 'ggstance', 'testthat', 'vdiffr'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggplotify', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'network'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Case_studies.Rmd' using rmarkdown
--- finished re-building 'Case_studies.Rmd'

--- re-building 'interlineaR.Rmd' using rmarkdown
Quitting from lines 16-23 (interlineaR.Rmd) 
Error: processing vignette 'interlineaR.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'interlineaR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'arm', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'NMF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readxl'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clinUtils', 'cowplot', 'dplyr', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'tibble', 'agricolae', 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mice', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'NMF', 'InterSIM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mgcv'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'ggplot2', 'Hmisc', 'memisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tibble', 'testthat'
Packages suggested but not available for checking:
  'iNZightPlots', 'testthat'
Package required but not available: 'iNZightTools'

Packages suggested but not available for checking:
  'viridis', 'testthat', 'ggplot2', 'dplyr', 'tidyr', 'forcats',
  'ggmosaic', 'waffle', 'ggthemes', 'ggbeeswarm', 'ggridges', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'dplyr', 'ggplot2', 'ggrepel', 'ggtext', 'iNZightPlots',
  'patchwork'

Packages suggested but not available for checking:
  'iNZightTools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'haven', 'readr', 'readxl', 'srvyr', 'styler',
  'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggtext', 'patchwork', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'colourpicker', 'kableExtra'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'eurostat', 'tidyr', 'forcats', 'kableExtra', 'tibble',
  'readxl'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringr'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'dplyr', 'fuzzyjoin', 'pillar', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'ipaddress-classes.Rmd' using rmarkdown
--- finished re-building 'ipaddress-classes.Rmd'

--- re-building 'ipaddress-examples.Rmd' using rmarkdown
Quitting from lines 11-16 (ipaddress-examples.Rmd) 
Error: processing vignette 'ipaddress-examples.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'ipaddress-examples.Rmd'

SUMMARY: processing the following file failed:
  'ipaddress-examples.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'treemap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'expm'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'testthat', 'eeptools', 'kableExtra', 'gtsummary',
  'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr', 'mlr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'randomForestSRC'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'caret', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'seqinr'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'haven', 'hipread', 'readr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'sf', 'testthat', 'dbplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggforce', 'ggplot2'

Package suggested but not available for checking: 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'IPWboxplot-Ex.R' failed
The error most likely occurred in:

> ### Name: IPW.ASYM.boxplot
> ### Title: Boxplot adapted to skewness and missing values
> ### Aliases: IPW.ASYM.boxplot
> ### Keywords: quantile boxplot missing inverse probability weighted
> 
> ### ** Examples
> 
> 
> ## A real data example
> 
> 
> library(mice)
Error in library(mice) : there is no package called 'mice'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Quitting from lines 46-55 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building 'my-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'MplusAutomation', 'tidyverse', 'dplyr', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'mlr', 'devtools'
Namespaces in Imports field not imported from:
  'coda' 'lattice'
  All declared Imports should be used.
Running examples in 'IRATER-Ex.R' failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
[1] 0
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
[1] 0
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Package required but not available: 'GGMncv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'repr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'DiagrammeR', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'getting-started-with-irg.Rmd' using rmarkdown
Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'DiagrammeR'
--- failed re-building 'getting-started-with-irg.Rmd'

SUMMARY: processing the following file failed:
  'getting-started-with-irg.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'ggsci'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("dplyr"): there is no package called 'dplyr'

See section 'Package namespaces' in the 'Writing R Extensions' manual.
Packages required but not available: 'repr', 'IRdisplay'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'irr'
  All declared Imports should be used.
Package required but not available: 'virtualspecies'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'BRugs'
Packages suggested but not available for checking:
  'ggplot2', 'sf', 'testthat'
Packages suggested but not available for checking:
  'dendextend', 'dplyr', 'ggplot2', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'isocat.Rmd' using rmarkdown
Quitting from lines 16-33 (isocat.Rmd) 
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'isocat.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tibble', 'dplyr', 'tidyr', 'readr'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'feather', 'readxl', 'rhdf5'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ibd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'dplyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'philentropy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'network', 'dplyr', 'cowplot', 'ggplot2', 'GGally', 'intergraph',
  'sna', 'networkDynamic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 45-47 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'NMF'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfortify', 'readr', 'janitor', 'ggcorrplot',
  'tidyr', 'broom', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'forecast', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rsample'

Package suggested but not available for checking: 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'AER'

Packages suggested but not available for checking: 'testthat', 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'locClass'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'gurobi', 'cplexAPI', 'testthat', 'AER', 'ggplot2'
Package required but not available: 'car'

Packages suggested but not available for checking:
  'AER', 'testthat', 'modelsummary', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'coala', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'jaatha-evolution.Rmd' using rmarkdown
Quitting from lines 26-33 (jaatha-evolution.Rmd) 
Error: processing vignette 'jaatha-evolution.Rmd' failed with diagnostics:
there is no package called 'coala'
--- failed re-building 'jaatha-evolution.Rmd'

--- re-building 'jaatha-intro.Rmd' using rmarkdown
--- finished re-building 'jaatha-intro.Rmd'

SUMMARY: processing the following file failed:
  'jaatha-evolution.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'qvalue', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'coala', 'scrm', 'testthat'
Package required but not available: 'mvp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ClusterR', 'qvalue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'JacobiEigen.Rmd' using rmarkdown
Quitting from lines 100-113 (JacobiEigen.Rmd) 
Error: processing vignette 'JacobiEigen.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'JacobiEigen.Rmd'

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

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

> ### Name: austen_books
> ### Title: Tidy data frame of Jane Austen's 6 completed, published novels
> ### Aliases: austen_books
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'sf', 'testthat', 'tibble', 'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'GA'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'cli', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rworldmap', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

Packages suggested but not available for checking:
  'dplyr', 'forecast', 'iClick', 'tibble', 'timetk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lvm4net', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'agricolae'
Package unavailable to check Rd xrefs: 'agricolae'
Packages required but not available:
  'car', 'ggplot2', 'GGally', 'afex', 'ggridges'

Packages suggested but not available for checking:
  'exact2x2', 'testthat', 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'jmv'
Error(s) in re-building vignettes:
--- re-building 'jmvReadWrite.Rmd' using rmarkdown

Attaching package: 'jmvReadWrite'

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

    ToothGrowth

Quitting from lines 69-80 (jmvReadWrite.Rmd) 
Error: processing vignette 'jmvReadWrite.Rmd' failed with diagnostics:
there is no package called 'jmv'
--- failed re-building 'jmvReadWrite.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'

Packages which this enhances but not available for checking:
  'mice', 'MRCE', 'remMap'
Packages suggested but not available for checking:
  'ggplot2', 'ggpubr', 'testthat'
Running examples in 'JointAI-Ex.R' failed
The error most likely occurred in:

> ### Name: densplot
> ### Title: Plot the posterior density from object of class JointAI
> ### Aliases: densplot densplot.JointAI
> 
> ### ** Examples
> 
> 
> # fit a JointAI object:
> mod <- lm_imp(y ~ C1 + C2 + M1, data = wideDF, n.iter = 100)
> 
> # Example 1: basic densityplot
> densplot(mod)
> densplot(mod, exclude_chains = 2)
> 
> 
> # Example 2: use vlines to mark zero
> densplot(mod, col = c("darkred", "darkblue", "darkgreen"),
+          vlines = list(list(v = rep(0, nrow(summary(mod)$res$y$regcoef)),
+                             col = grey(0.8))))
> 
> 
> # Example 3: use vlines to visualize posterior mean and 2.5%/97.5% quantiles
> res <- rbind(summary(mod)$res$y$regcoef[, c('Mean', '2.5%', '97.5%')],
+              summary(mod)$res$y$sigma[, c('Mean', '2.5%', '97.5%'),
+              drop = FALSE]
+              )
> densplot(mod, vlines = list(list(v = res[, "Mean"], lty = 1, lwd = 2),
+                             list(v = res[, "2.5%"], lty = 2),
+                             list(v = res[, "97.5%"], lty = 2)))
> 
> 
> # Example 4: ggplot version
> densplot(mod, use_ggplot = TRUE)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: densplot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: 'mitml'
Packages required but not available: 'SpATS', 'fds', 'ggplot2', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'doParallel'
  All declared Imports should be used.
Package required but not available: 'cli'

Packages suggested but not available for checking: 'badger', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaflet', 'sf', 'tibble'

Packages suggested but not available for checking:
  'lintr', 'lwgeom', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'ggsci'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'dplyr', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'jstable', 'labelled', 'GGally', 'ggplot2', 'haven',
  'tableone', 'jskm', 'geepack', 'timeROC', 'Hmisc', 'see', 'readr',
  'ggpubr'

Packages suggested but not available for checking: 'testthat', 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'cli', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pillar', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'repurrrsive', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geepack', 'labelled', 'tableone', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'broom', 'broom.mixed', 'ggstance', 'kableExtra', 'lmerTest',
  'pbkrtest', 'weights', 'testthat'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rvest', 'SwimmeR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RcppParallel', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DiagrammeR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggthemes', 'ggplot2', 'ggpubr', 'mice', 'rms'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'clustMD', 'ggplot2', 'Hmisc'
Package required but not available: 'biomaRt'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MVN', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'forcats', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'roll'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'univariateML'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #
  > # The Hadley-verse is an amazing place: unit testing via testthat
  > # See also  http://r-pkgs.had.co.nz/tests.html
  > #
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespaces in Imports field not imported from:
  'lme4' 'metafor' 'nlme'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(kerasR)
  Loading required package: kerasR
  
  python not available
  See reticulate::use_python() to set python path, 
  then use kerasR::keras_init() to retry
  > 
  > test_check("kerasR")
  Error in test_check("kerasR") : could not find function "test_check"
  Execution halted
Packages required but not available:
  'plotly', 'tidyjson', 'dplyr', 'echarts4r'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'testthat'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test_parallel.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'ICtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'benchmarkme', 'dplyr', 'ggplot2', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'quanteda', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'readtext', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using knitr
Loading required package: knitr
Loading required package: kfigr
knitr hook "anchor" is now available
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 26-28 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
could not find function "qplot"
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'fdapace', 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'vdiffr'
Running examples in 'khroma-Ex.R' failed
The error most likely occurred in:

> ### Name: scale_crameri_cyclic
> ### Title: Fabio Crameri's Cyclic Color Schemes for 'ggplot2'
> ### Aliases: scale_crameri_cyclic scale_colour_brocO scale_color_brocO
> ###   scale_fill_brocO scale_colour_corkO scale_color_corkO
> ###   scale_fill_corkO scale_colour_vikO scale_color_vikO scale_fill_vikO
> ###   scale_colour_romaO scale_color_romaO scale_fill_romaO
> ###   scale_colour_bamO scale_color_bamO scale_fill_bamO
> 
> ### ** Examples
> 
> data(economics, package = "ggplot2")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'ggplot2'
Calls: data -> find.package
Execution halted
Packages required but not available:
  'rio', 'tibble', 'dplyr', 'tidyr', 'Rsamtools', 'rtracklayer'

Packages suggested but not available for checking:
  'ggplot2', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'readr', 'ggrepel', 'tibble', 'plotly', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'example.Rmd' using rmarkdown
Quitting from lines 131-136 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'example.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'tibble', 'testthat'
Running examples in 'kitagawa-Ex.R' failed
The error most likely occurred in:

> ### Name: cross_spectrum
> ### Title: Calculate the cross-spectrum of two timeseries
> ### Aliases: cross_spectrum cross_spectrum.mts cross_spectrum.default
> 
> ### ** Examples
> 
> require(stats)
> require(psd)
Loading required package: psd
Loaded psd (2.1.0) -- Adaptive multitaper spectrum estimation; to start, see ?pspectrum
> 
> n <- 1000
> ramp <- seq_len(n)
> parab <- ramp^2
> 
> set.seed(1255)
> X <- ts(rnorm(n) + ramp/2)
> Y <- ts(rnorm(n) + ramp/10 + parab/100)
> 
> # Calculate the multitaper cross spectrum
> csd <- cross_spectrum(X, Y, k=20)
Error in loadNamespace(x) : there is no package called 'tibble'
Calls: cross_spectrum ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
Re-running with no redirection of stdout/stderr.
Package required but not available: 'questionr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Rcpp' 'SnowballC' 'stringi'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'klsh.Rmd' using rmarkdown
Loading required package: stringdist
Loading required package: plyr
Quitting from lines 163-179 (klsh.Rmd) 
Error: processing vignette 'klsh.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'klsh.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'dendextend', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'kmer-vignette.Rmd' using rmarkdown
Quitting from lines 140-160 (kmer-vignette.Rmd) 
Error: processing vignette 'kmer-vignette.Rmd' failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building 'kmer-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'cowplot', 'ggplot2', 'pammtools', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'devtools', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tibble', 'styler'
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testit)
  > test_pkg("knitr")
  Error from withRestarts(stop(cond), retry_loadNamespace = function() NULL) 
  Error in loadNamespace(x) : there is no package called 'tibble'
  Calls: test_pkg ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'parallelDist', 'forecast'

Package suggested but not available for checking: 'tsibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'caret', 'psycho'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'doMC'
Package suggested but not available for checking: 'rgbif'
Packages required but not available: 'sf', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'broom.mixed', 'dplyr', 'ggplot2', 'mice', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'pbkrtest', 'devtools', 'forcats', 'roxygen2', 'testthat', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', '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'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ../inst/tests
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_check("koRpus")
  Error in test_check("koRpus") : could not find function "test_check"
  Execution halted
Package required but not available: 'emstreeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'FactoClass', 'LICORS', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ##
  > ##  Unit testing file
  > ##
  > ##  Created by Daniel Rodriguez Perez on 7/12/2014.
  > ##
  > ##  Copyright (c) 2014 Daniel Rodriguez Perez.
  > ##
  > ##  This program is free software: you can redistribute it and/or modify
  > ##  it under the terms of the GNU General Public License as published by
  > ##  the Free Software Foundation, either version 3 of the License, or
  > ##  (at your option) any later version.
  > ##
  > ##  This program is distributed in the hope that it will be useful,
  > ##  but WITHOUT ANY WARRANTY; without even the implied warranty of
  > ##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > ##  GNU General Public License for more details.
  > ##
  > ##  You should have received a copy of the GNU General Public License
  > ##  along with this program.  If not, see <http://www.gnu.org/licenses/>
  > ## 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'GSE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RUnit'
  All declared Imports should be used.
Packages required but not available: 'haven', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'questionr'

Package which this enhances but not available for checking: 'memisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'tests-all.R'
Running the tests in 'tests/tests-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'labelVector.Rmd' using knitr
Quitting from lines 124-133 (labelVector.Rmd) 
Error: processing vignette 'labelVector.Rmd' failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building 'labelVector.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'Rcmdr'
Package unavailable to check Rd xrefs: 'factoextra'
Packages required but not available: 'dplyr', 'janitor', 'sjmisc'

Packages suggested but not available for checking:
  'testthat', 'httptest', 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'run_testthattests.R'
Running the tests in 'tests/run_testthattests.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'sf', 'tibble', 'tidyr', 'qs'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spatialreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'readr', 'bestNormalize', 'imputeTS', 'torch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'lamW'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GGally', 'intergraph', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mlr'

Packages suggested but not available for checking: 'spdep', 'plotKML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'ggplot2', 'tibble'

Packages suggested but not available for checking: 'dplyr', 'testthat'

Packages which this enhances but not available for checking: 'stars', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'sf', 'testthat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rms', 'Hmisc', 'lmerTest'
Packages required but not available: 'lintr', 'repr', 'roxygen2', 'styler'

Packages suggested but not available for checking: 'mockery', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Vignette_for_LA.Rmd' using rmarkdown
Quitting from lines 25-27 (Vignette_for_LA.Rmd) 
Error: processing vignette 'Vignette_for_LA.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'Vignette_for_LA.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'patchwork', 'rvest', 'tidyr'

Packages suggested but not available for checking:
  'DALEX', 'forecast', 'ggforce', 'ggrepel', 'googleAuthR',
  'googlesheets4', 'plotly', 'rdrop2', 'rtweet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'config.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'network', 'ergm', 'sna'

Packages suggested but not available for checking:
  'heplots', 'ergm.userterms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # See https://github.com/r-lib/testthat/issues/86
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tibble'
Packages required but not available: 'ggplot2', 'caret'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'fda', 'funFEM', 'akmedoids', 'dtwclust',
  'qqplotr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mpoly', 'ggplot2', 'dplyr', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spdep', 'spatialreg', 'sf'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'mice'
Packages suggested but not available for checking:
  'fields', 'geepack', 'gof', 'lava.tobit', 'lavaSearch2', 'testthat'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > #library("lava")
  > suppressPackageStartupMessages(library("testthat"))
  Error in library("testthat") : there is no package called 'testthat'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'lmerTest', 'pbkrtest', 'riskRegression', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'revdbayes'

Packages suggested but not available for checking:
  'eva', 'testthat', 'texmex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'dipsaus'
Packages required but not available: 'vapour', 'quadmesh'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'tibble', 'dbplyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'dplyr', 'tibble', 'ggplot2', 'ReinforcementLearning'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'pkgbuild'
Error(s) in re-building vignettes:
--- re-building 'lbfgsb3c.Rmd' using rmarkdown
Quitting from lines 18-21 (lbfgsb3c.Rmd) 
Error: processing vignette 'lbfgsb3c.Rmd' failed with diagnostics:
there is no package called 'pkgbuild'
--- failed re-building 'lbfgsb3c.Rmd'

SUMMARY: processing the following file failed:
  'lbfgsb3c.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'trekcolors'

Packages suggested but not available for checking:
  'testthat', 'ggrepel', 'leaflet', 'leaflet.extras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fdapace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'ggplot2', 'broom', 'semPlot'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dendextend'

Packages suggested but not available for checking: 'testthat', 'tosca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'highcharter', 'ldatuning', 'plotly', 'quanteda',
  'tidyr', 'tidytext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'tests.R'
Running the tests in 'tests/tests.R' failed.
Complete output:
  > library(ldat)
  Loading required package: lvec
  
  Attaching package: 'lvec'
  
  The following object is masked from 'package:base':
  
      order
  
  Loading required package: Rcpp
  
  Attaching package: 'ldat'
  
  The following objects are masked from 'package:base':
  
      append, match, table, which
  
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'viridis'

Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gistr'
Packages suggested but not available for checking:
  'rtracklayer', 'ggplot2', 'vcfR'
Package unavailable to check Rd xrefs: 'vcfR'
Packages required but not available: 'ecd', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'updog', 'VariantAnnotation'
Package unavailable to check Rd xrefs: 'updog'
Packages suggested but not available for checking:
  'GA', 'testthat', 'ggplot2', 'patchwork'
Error(s) in re-building vignettes:
--- re-building 'ldsr.Rmd' using rmarkdown
Quitting from lines 48-52 (ldsr.Rmd) 
Error: processing vignette 'ldsr.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ldsr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'leaflet'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaflet', 'sf'

Packages suggested but not available for checking: 'leafgl', 'stars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaflet', 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaflet', 'leaflet.extras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'leaflet'

Packages suggested but not available for checking: 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'leaflet'

Package suggested but not available for checking: 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'leaflet'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'leaflet', 'testthat'
Running examples in 'leaflet.multiopacity-Ex.R' failed
The error most likely occurred in:

> ### Name: addOpacityControls
> ### Title: Add Opacity Controls
> ### Aliases: addOpacityControls
> 
> ### ** Examples
> 
> # Load libraries
> library(leaflet)
Error in library(leaflet) : there is no package called 'leaflet'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'usage-leaflet.Rmd' using rmarkdown
Quitting from lines 18-27 (usage-leaflet.Rmd) 
Error: processing vignette 'usage-leaflet.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building 'usage-leaflet.Rmd'

--- re-building 'usage-leafletProxy.Rmd' using rmarkdown
--- finished re-building 'usage-leafletProxy.Rmd'

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

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

> ### Name: addHigherOpacity
> ### Title: Add higher opacity control to map
> ### Aliases: addHigherOpacity
> 
> ### ** Examples
> 
> # Libraries
> library(leaflet)
Error in library(leaflet) : there is no package called 'leaflet'
Execution halted
Package required but not available: 'viridis'

Packages suggested but not available for checking: 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'leaflet', 'sf'

Package suggested but not available for checking: 'testthat'

Packages which this enhances but not available for checking:
  'geojsonio', 'mapedit', 'mapview'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Package suggested but not available for checking: 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lidR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'leaflet'

Package suggested but not available for checking: 'geojsonio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'LEAP_Vignette.Rnw' using Sweave

Error: processing vignette 'LEAP_Vignette.Rnw' failed with diagnostics:
 chunk 10 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'LEAP_Vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'readxl', 'haven', 'readODS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'roxygen2', 'devtools'
Packages required but not available: 'ggplot2', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rio', 'tidyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'attn.Rmd' using rmarkdown
Quitting from lines 12-16 (attn.Rmd) 
Error: processing vignette 'attn.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'attn.Rmd'

--- re-building 'bills.Rmd' using rmarkdown
Quitting from lines 12-16 (bills.Rmd) 
Error: processing vignette 'bills.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'bills.Rmd'

--- re-building 'hansard.Rmd' using rmarkdown
Quitting from lines 12-16 (hansard.Rmd) 
Error: processing vignette 'hansard.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'hansard.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 12-15 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'introduction.Rmd'

--- re-building 'schedule.Rmd' using rmarkdown
Quitting from lines 12-16 (schedule.Rmd) 
Error: processing vignette 'schedule.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'schedule.Rmd'

--- re-building 'voting.Rmd' using rmarkdown
Quitting from lines 12-16 (voting.Rmd) 
Error: processing vignette 'voting.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'voting.Rmd'

SUMMARY: processing the following files failed:
  'attn.Rmd' 'bills.Rmd' 'hansard.Rmd' 'introduction.Rmd'
  'schedule.Rmd' 'voting.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'greybox', 'smooth'

Packages suggested but not available for checking:
  'Mcomp', 'testthat', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sccore'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'bipartite', 'devtools', 'network', 'testthat', 'tibble'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'sf', 'testthat', 'viridis'
Package suggested but not available for checking: 'haven'
Package unavailable to check Rd xrefs: 'MESS'
Package required but not available: 'syuzhet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quanteda', 'quanteda.textstats', 'tibble'

Packages suggested but not available for checking:
  'corpustools', 'dplyr', 'testthat', 'tidytext', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shinyFiles', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'anomalies.R'
  Comparing 'anomalies.Rout' to 'anomalies.Rout.save' ... OK
  Running 'bctest.R'
  Comparing 'bctest.Rout' to 'bctest.Rout.save' ... OK
  Running 'cgsolve.R'
  Comparing 'cgsolve.Rout' to 'cgsolve.Rout.save' ... OK
  Running 'cluster.R'
  Comparing 'cluster.Rout' to 'cluster.Rout.save' ... OK
  Running 'comparelm.R'
  Comparing 'comparelm.Rout' to 'comparelm.Rout.save' ... OK
  Running 'degenerate.R'
  Comparing 'degenerate.Rout' to 'degenerate.Rout.save' ... OK
  Running 'efcheck.R'
  Comparing 'efcheck.Rout' to 'efcheck.Rout.save' ... OK
  Running 'fourfac.R'
  Comparing 'fourfac.Rout' to 'fourfac.Rout.save' ... OK
  Running 'intact.R'
  Comparing 'intact.Rout' to 'intact.Rout.save' ... OK
  Running 'interact.R'
  Comparing 'interact.Rout' to 'interact.Rout.save' ... OK
  Running 'ivtest.R'
  Comparing 'ivtest.Rout' to 'ivtest.Rout.save' ... OK
  Running 'lfetest.R'
  Comparing 'lfetest.Rout' to 'lfetest.Rout.save' ... OK
  Running 'mlhs.R'
  Comparing 'mlhs.Rout' to 'mlhs.Rout.save' ... OK
  Running 'multiway.R'
  Comparing 'multiway.Rout' to 'multiway.Rout.save' ... OK
  Running 'naomit.R'
  Comparing 'naomit.Rout' to 'naomit.Rout.save' ... OK
  Running 'nonest.R'
  Comparing 'nonest.Rout' to 'nonest.Rout.save' ... OK
  Running 'onefac.R'
  Comparing 'onefac.Rout' to 'onefac.Rout.save' ... OK
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'forecast'

Packages suggested but not available for checking: 'testthat', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'bayesplot', 'ggplot2',
  'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'gmailr', 'RMariaDB', 'rsyslog', 'testthat'
Packages unavailable to check Rd xrefs: 'gmailr', 'rsyslog'
Packages suggested but not available for checking:
  'cli', 'testthat', 'tibble'
Packages unavailable to check Rd xrefs: 'tibble', 'cli'
Error(s) in re-building vignettes:
--- re-building 'Vignette_for_LHD.Rmd' using rmarkdown
Quitting from lines 26-28 (Vignette_for_LHD.Rmd) 
Error: processing vignette 'Vignette_for_LHD.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'Vignette_for_LHD.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'assertr', 'testthat'
Packages required but not available:
  'readr', 'readxl', 'haven', 'dplyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'libstableR-Ex.R' failed
The error most likely occurred in:

> ### Name: libstableR
> ### Title: LibstableR: Fast and accurate evaluation, random number
> ###   generation and parameter estimation of skew stable distributions.
> ### Aliases: libstableR libstableR-package
> ### Keywords: package
> 
> ### ** Examples
> 
> # Set alpha, beta, sigma and mu stable parameters in a vector
> pars <- c(1.5, 0.9, 1, 0)
> 
> # Generate an abscissas axis and probabilities vector
> x <- seq(-5, 10, 0.05)
> p <- seq(0.01, 0.99, 0.01)
> 
> # Calculate pdf, cdf and quantiles
> pdf <- stable_pdf(x, pars)
Packages required but not available: 'car', 'reldist', 'lidR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'concaveman', 'mapview', 'mapedit', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'markovchain'

Packages suggested but not available for checking:
  'demography', 'forecast', 'testthat', 'StMoMo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'communicate.Rmd' using rmarkdown
--- finished re-building 'communicate.Rmd'

--- re-building 'manage.Rmd' using rmarkdown
Quitting from lines 34-38 (manage.Rmd) 
Error: processing vignette 'manage.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'manage.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'dplyr', 'modelr', 'tidyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'curl' 'jsonlite'
  All declared Imports should be used.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/lightgbm/lightgbm.Rcheck/00install.out' for details.
Packages required but not available: 'tibble', 'dplyr', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'caret', 'dplyr', 'ggplot2', 'M3C', 'RCy3', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ddpcr', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'readr', 'textclean'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'mlr', 'sessioninfo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tourr', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lamW'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'factoextra', 'ggplot2', 'sparsevar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'viridis', 'tidyr', 'readr', 'forecast'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'roxygen2', 'devtools', 'testthat'
Packages required but not available: 'leaflet', 'leaflet.minicharts'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'tidyr'
Packages required but not available: 'devtools', 'roxygen2', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'intergraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'testthat'

Package suggested but not available for checking: 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'shadowtext', 'tableone', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'listcompr-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.logical.and
> ### Title: Generate Logical Conditions with List Comprehension
> ### Aliases: gen.logical.and gen.logical.or
> 
> ### ** Examples
> 
> # Returns a_1 == 1 & a_2 == 2 & a_3 == 3
> gen.logical.and(a_i == i, i = 1:3)
a_1 == 1L & (a_2 == 2L & a_3 == 3L)
> 
> # A data frame of tuples (x_1, x_2, x_3, x_4) summing up to 10 with x_i <= x_(i+1)
> gen.data.frame(c(x_1, ..., x_4), x_ = 1:10, x_1 + ... + x_4 == 10, 
+                gen.logical.and(x_i <= x_(i+1), i = 1:3))
  x_1 x_2 x_3 x_4
1   2   2   3   3
2   1   3   3   3
3   2   2   2   4
4   1   2   3   4
5   1   1   4   4
6   1   2   2   5
7   1   1   3   5
8   1   1   2   6
9   1   1   1   7
> 
> # Get all permutations of 1:4
> gen.data.frame(c(a_1, ..., a_4), a_ = 1:4, 
+                gen.logical.and(a_i != a_j, i = 1:4, j = (i+1):4))
   a_1 a_2 a_3 a_4
1    4   3   2   1
2    3   4   2   1
3    4   2   3   1
4    2   4   3   1
5    3   2   4   1
6    2   3   4   1
7    4   3   1   2
8    3   4   1   2
9    4   1   3   2
10   1   4   3   2
11   3   1   4   2
12   1   3   4   2
13   4   2   1   3
14   2   4   1   3
15   4   1   2   3
16   1   4   2   3
17   2   1   4   3
18   1   2   4   3
19   3   2   1   4
20   2   3   1   4
21   3   1   2   4
22   1   3   2   4
23   2   1   3   4
24   1   2   3   4
>                
> # Get again the permutations of 1:4, using filter from dplyr 
> df <- gen.data.frame(c(a_1, ..., a_4), a_ = 1:4)
> dplyr::filter(df, !!gen.logical.and(a_i != a_j, i = 1:3, j = (i+1):4))
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 132-135 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'listdown.rmd' using rmarkdown
Quitting from lines 55-70 (listdown.rmd) 
Error: processing vignette 'listdown.rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'listdown.rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'arm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'dplyr', 'breakDown', 'forestmodel', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'DALEX'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mlr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'StanHeaders', 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'reghelper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dynutils'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'pbkrtest', 'car'
Packages unavailable to check Rd xrefs: 'pbkrtest', 'car'
Running 'AAAtest-all.R'
  Running 'HSAURtrees.R'
  Running 'REMLdev.R'
  Running 'ST.R'
  Running 'agridat_gotway.R'
  Running 'bootMer.R'
  Running 'boundary.R'
  Running 'confint.R'
  Running 'devCritFun.R'
  Running 'drop.R'
  Running 'drop1contrasts.R'
  Running 'dynload.R'
  Running 'elston.R'
  Running 'evalCall.R'
  Running 'extras.R'
  Running 'falsezero_dorie.R'
  Running 'fewlevels.R'
  Running 'getME.R'
  Running 'glmer-1.R'
  Running 'glmerControlPass.R'
  Running 'glmerWarn.R'
  Running 'glmmExt.R'
  Running 'glmmWeights.R'
  Running 'hatvalues.R'
  Running 'is.R'
  Running 'lmList-tst.R'
  Running 'lme4_nlme.R'
  Running 'lmer-0.R'
  Running 'lmer-1.R'
  Comparing 'lmer-1.Rout' to 'lmer-1.Rout.save' ... OK
  Running 'lmer-conv.R'
  Running 'lmer2_ex.R'
  Running 'methods.R'
  Running 'minval.R'
  Running 'modFormula.R'
  Running 'nbinom.R'
  Running 'nlmer-conv.R'
  Running 'nlmer.R'
  Comparing 'nlmer.Rout' to 'nlmer.Rout.save' ... OK
  Running 'offset.R'
  Running 'optimizer.R'
  Running 'polytomous.R'
  Running 'prLogistic.R'
  Running 'predict_basis.R'
  Running 'predsim.R'
  Running 'priorWeights.R'
  Running 'priorWeightsModComp.R'
  Running 'profile-tst.R'
Running the tests in 'tests/profile-tst.R' failed.
Complete output:
  > library(lme4)
  Loading required package: Matrix
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'lmerperf.Rmd' using rmarkdown
Loading required package: Matrix
--- finished re-building 'lmerperf.Rmd'

--- re-building 'Theory.Rnw' using knitr
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'Theory.Rnw'

--- re-building 'lmer.Rnw' using knitr
Quitting from lines 95-111 (lmer.Rnw) 
Error: processing vignette 'lmer.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'lmer.Rnw'

--- re-building 'PLSvGLS.Rnw' using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'PLSvGLS.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'scdhlm', 'dplyr', 'tidyr'
Running examples in 'lmeInfo-Ex.R' failed
The error most likely occurred in:

> ### Name: g_mlm
> ### Title: Calculates adjusted mlm effect size
> ### Aliases: g_mlm
> 
> ### ** Examples
> 
> 
> library(nlme)
> data(Bryant2016, package = "lmeInfo")
> Bryant2016_RML1 <- lme(fixed = outcome ~ treatment,
+                        random = ~ 1 | school/case,
+                        correlation = corAR1(0, ~ session | school/case),
+                        data = Bryant2016)
> Bryant2016_g1 <- g_mlm(Bryant2016_RML1, p_const = c(0,1), r_const = c(1,1,0,1),
+                        infotype = "expected", returnModel = TRUE)
> summary(Bryant2016_g1)
                                           est      se
Tau.school.school.var((Intercept))     105.619 285.200
Tau.case.case.var((Intercept))           0.000 632.159
cor_params                               0.978   0.015
sigma_sq                              1058.303 678.388
total variance                        1163.922 366.515
(Intercept)                             84.571   9.684
treatmenttreatment                      16.425   2.975
treatment effect at a specified time    16.425   2.975
unadjusted effect size                   0.481   0.122
adjusted effect size                     0.463   0.118
degree of freedom                       20.169        
constant kappa                           0.087        
logLik                               -1133.122        
> print(Bryant2016_g1)
                          est    se
unadjusted effect size  0.481 0.122
adjusted effect size    0.463 0.118
degree of freedom      20.169      
> 
> data(Laski, package = "scdhlm")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'scdhlm'
Calls: data -> find.package
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggdist', 'HLMdiag', 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'pbkrtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mnormt'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'SPEI'
Packages required but not available: 'car', 'pbkrtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'dynlm', 'AER'
Package required but not available: 'cli'

Packages suggested but not available for checking: 'testthat', 'twang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenStreetMap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'pillar', 'pkgdown', 'testthat'
Running examples in 'LocalControl-Ex.R' failed
The error most likely occurred in:

> ### Name: LocalControl
> ### Title: Local Control
> ### Aliases: LocalControl
> 
> ### ** Examples
> 
>  # cross-sectional
> 
>  data(lindner)
>  linVars <- c("stent", "height", "female", "diabetic", "acutemi",
+               "ejecfrac", "ves1proc")
>  csresults = LocalControl(data = lindner,
+                           clusterVars = linVars,
+                           treatmentColName = "abcix",
+                           outcomeColName = "cardbill",
+                           treatmentCode = 1)
Processing 0
Errors in running code in vignettes:
when running code in 'LocalControl-jss-2018.Rnw'

> options(prompt = "R> ", continue = "+  ", width = 70, 
+     useFancyQuotes = FALSE)

> doCalcs = F

> if (!require("data.table")) {
+     install.packages("data.table")
+     library("data.table")
+ }
Loading required package: data.table

> if (!require("colorspace")) {
+     install.packages("colorspace")
+     library("colorspace")
+ }
Loading required package: colorspace

> if (!require("RColorBrewer")) {
+     install.packages("RColorBrewer")
+     library("RColorBrewer")
+ }
Loading required package: RColorBrewer

> if (!require("gridExtra")) {
+     install.packages("gridExtra")
+     library("gridExtra")
+ }
Loading required package: gridExtra

> if (!require("ggplot2")) {
+     install.packages("ggplot2")
+     library("ggplot2")
+ }
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Installing package into 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/LocalControl/LocalControl.Rcheck'
(as 'lib' is unspecified)

  When sourcing 'LocalControl-jss-2018.R':
Error: trying to use CRAN without setting a mirror
Execution halted

  'LocalControl-jss-2018.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'LocalControl-jss-2018.Rnw' using Sweave
Loading required package: data.table
Loading required package: colorspace
Loading required package: RColorBrewer
Loading required package: gridExtra
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Installing package into 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/LocalControl/LocalControl.Rcheck'
(as 'lib' is unspecified)

Error: processing vignette 'LocalControl-jss-2018.Rnw' failed with diagnostics:
 chunk 2 (label = init_libs_vars_calcs) 
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror

--- failed re-building 'LocalControl-jss-2018.Rnw'

SUMMARY: processing the following file failed:
  'LocalControl-jss-2018.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'sampleSelection'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ingredients'

Packages suggested but not available for checking: 'DALEX', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mosaic'
Package required but not available: 'expectreg'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'metR', 'viridis'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'distr'
  All declared Imports should be used.
Package in Depends field not imported from: 'logcondens'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking:
  'slackr', 'testthat', 'devtools', 'roxygen2', 'rsyslog'
Running 'run_tests.R'
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'logitnorm.Rmd' using knitr
Quitting from lines 7-30 (logitnorm.Rmd) 
Error: processing vignette 'logitnorm.Rmd' failed with diagnostics:
could not find function "exit"
--- failed re-building 'logitnorm.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'fastDummies', 'ggplot2', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'basic_usage.Rmd' using rmarkdown
NOTE: Using results from run 10 of 10 multistart runs
(the run with the largest log-likelihood value)
NOTE: Using results from run 10 of 10 multistart runs
(the run with the largest log-likelihood value)
--- finished re-building 'basic_usage.Rmd'

--- re-building 'data_formatting.Rmd' using rmarkdown
Quitting from lines 62-63 (data_formatting.Rmd) 
Error: processing vignette 'data_formatting.Rmd' failed with diagnostics:
there is no package called 'fastDummies'
--- failed re-building 'data_formatting.Rmd'

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

--- re-building 'mnl_models.Rmd' using rmarkdown
NOTE: Using results from run 10 of 10 multistart runs
(the run with the largest log-likelihood value)
--- finished re-building 'mnl_models.Rmd'

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

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

--- re-building 'predict_choices.Rmd' using rmarkdown
Quitting from lines 175-192 (predict_choices.Rmd) 
Error: processing vignette 'predict_choices.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'predict_choices.Rmd'

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

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

SUMMARY: processing the following files failed:
  'data_formatting.Rmd' 'predict_choices.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # workaround for error LC_CTYPE failed, using "C" but does not work
  > #https://github.com/r-lib/testthat/issues/86
  > #Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'lognorm.Rmd' using rmarkdown
Quitting from lines 17-40 (lognorm.Rmd) 
Error: processing vignette 'lognorm.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'lognorm.Rmd'

--- re-building 'lognormalDiff.Rmd' using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'lognormalDiff.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building 'lognormalDiff.Rmd'

--- re-building 'lognormalSum.Rmd' using rmarkdown
Quitting from lines 16-39 (lognormalSum.Rmd) 
Error: processing vignette 'lognormalSum.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'lognormalSum.Rmd'

SUMMARY: processing the following files failed:
  'lognorm.Rmd' 'lognormalSum.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'tidylog', 'dplyr'
Packages required but not available: 'network', 'ggplot2', 'intergraph'

Packages suggested but not available for checking: 'testthat', 'ergm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'TDAstats', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggmulti', 'GGally'

Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'tibble', 'testthat', 'nycflights13'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rworldmap', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'loon.ggplot', 'colourpicker'

Packages suggested but not available for checking:
  'dplyr', 'ggmulti', 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tourr', 'loon.ggplot', 'tibble'

Packages suggested but not available for checking: 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'bayesplot', 'brms', 'ggplot2', 'rstan', 'rstanarm', 'rstantools',
  'spdep', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(loo)
  This is loo version 2.4.1
  - Online documentation and vignettes at mc-stan.org/loo
  - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. 
  - Windows 10 users: loo may be very slow if 'mc.cores' is set in your .Rprofile file (see https://github.com/stan-dev/loo/issues/94).
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'biomaRt', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dineq'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geomorph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat) # nolint
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'lotri-motivation.Rmd' using rmarkdown
Quitting from lines 36-42 (lotri-motivation.Rmd) 
Error: processing vignette 'lotri-motivation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'lotri-motivation.Rmd'

SUMMARY: processing the following file failed:
  'lotri-motivation.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'virtualspecies'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'lphom-Ex.R' failed
The error most likely occurred in:

> ### Name: error_lphom
> ### Title: Global error of a lphom estimated table
> ### Aliases: error_lphom
> 
> ### ** Examples
> 
> mt.lphom <- lphom(France2017P[, 1:8], France2017P[, 9:12], "raw", NULL, FALSE)
*********************WARNING*********************
You are in a "raw" scenario.
The sums (by row) of origin and destination data differ. It is, for at least a spatial unit, the total number of electors in both elections is not the same. 

 To guarantee the matching: A new category of census entries (NET_ENTRIES) is included in the origin election and a new category of census exits (NET_EXITS) is also included in the destination election.

 %NET_ENTRIES=0.0281014834498004%
 %NET_EXITS=0.026247806955692%

 If NET_ENTRIES and/or NET_EXITS are really small, less than 1% in all units, their results will not be displayed in VTM, they are included in VTM.complete

 See paper "A model to estimate voter transitions from aggregated data. Application to 2017 French presidential elections" for details. 
*************************************************
> set.seed(253443)
> example <- error_lphom(mt.lphom, upper.alfa = 0.10, show.plot = FALSE, num.d = 5, B = 8)
Error: Package ggplot2 needed for this function to work. Please install it.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'ggpubr'

Packages suggested but not available for checking: 'testthat', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'LPGraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'LPGraph', 'LPBkg', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'ggplot2', 'devtools'
Error(s) in re-building vignettes:
--- re-building 'LPWC.Rmd' using rmarkdown
Quitting from lines 146-174 (LPWC.Rmd) 
Error: processing vignette 'LPWC.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'LPWC.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'Hmisc'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds', 'mice', 'car', 'mitml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'LICORS', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sensitivity', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'LSMRealOptions.Rmd' using rmarkdown
Quitting from lines 266-281 (LSMRealOptions.Rmd) 
Error: processing vignette 'LSMRealOptions.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'LSMRealOptions.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'lspline.Rmd' using rmarkdown
Quitting from lines 69-75 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'lspline.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'quanteda', 'quanteda.textstats', 'proxyC', 'ggplot2', 'ggrepel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'etable'
Packages suggested but not available for checking: 'ggmcmc', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'custom-models.Rmd' using knitr
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
--- finished re-building 'custom-models.Rmd'

--- re-building 'example-plots.Rmd' using knitr
Quitting from lines 13-17 (example-plots.Rmd) 
Error: processing vignette 'example-plots.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'example-plots.Rmd'

SUMMARY: processing the following file failed:
  'example-plots.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'arm'
Error(s) in re-building vignettes:
--- re-building 'DeterministicFunctions.Rmd' using rmarkdown
--- finished re-building 'DeterministicFunctions.Rmd'

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

--- re-building 'ltmle-MSM.Rmd' using rmarkdown
--- finished re-building 'ltmle-MSM.Rmd'

--- re-building 'ltmle-intro.Rmd' using rmarkdown
Failed with error:  'there is no package called 'arm''
Failed with error:  'there is no package called 'arm''
Quitting from lines 77-78 (ltmle-intro.Rmd) 
Error: processing vignette 'ltmle-intro.Rmd' failed with diagnostics:


Error occured during call to SuperLearner:
 A ~ W1 + W2 + W3  
 The error reported is:
 Error : You have selected bayesglm as a library algorithm but either do not have the arm package installed or it can not be loaded

--- failed re-building 'ltmle-intro.Rmd'

SUMMARY: processing the following file failed:
  'ltmle-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'randomForestSRC'
Namespaces in Imports field not imported from:
  'Icens' 'interval'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)
  +   test_check("lubridate")
  + }
  Error in packageVersion("testthat") : 
    there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'rpostgis'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'broom', 'dplyr', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'lucid_examples.Rmd' using rmarkdown
Loading required package: lucid
Loading required package: lattice
Quitting from lines 172-175 (lucid_examples.Rmd) 
Error: processing vignette 'lucid_examples.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building 'lucid_examples.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'ncdf4' 'raster'
  All declared Imports should be used.
Packages suggested but not available for checking: 'caret', 'Hmisc'
Packages unavailable to check Rd xrefs: 'Hmisc', 'caret'
Running examples in 'lulcc-Ex.R' failed
The error most likely occurred in:

> ### Name: allow
> ### Title: Implement decision rules for land use change
> ### Aliases: allow
> 
> ### ** Examples
> 
> 
> ## Plum Island Ecosystems
> 
> ## load observed land use data
> obs <- ObsLulcRasterStack(x=pie,
+                    pattern="lu",
+                    categories=c(1,2,3),
+                    labels=c("forest","built","other"),
+                    t=c(0,6,14))
> 
> ## get land use values
> x <- getValues(obs[[1]])
> x <- x[!is.na(x)]
> 
> ## create vector of arbitrary land use history values
> hist <- sample(1:10, length(x), replace=TRUE)
> 
> ## calculate demand and get change direction for first timestep
> dmd <- approxExtrapDemand(obs=obs, tout=0:14)
Warning in total(x = obs) :
  missing argument 'categories': getting categories from 'x'
Error in loadNamespace(x) : there is no package called 'Hmisc'
Calls: approxExtrapDemand ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted