'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for 'kmeans'
kmeansN: no visible global function definition for 'aggregate'
kmeansN2: no visible global function definition for 'aggregate'
kmeansN2: no visible binding for global variable 'sd'
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title 'Vignette Title':
  'ZipRadius.Rmd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'xtable', 'pbapply'

Packages suggested but not available for checking: 'randomForest', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'networkD3', 'shiny', 'shinydashboard', 'magrittr', 'Bios2cor',
  'seqinr', 'plotly', 'Hmisc'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'XML', 'curl', 'readr', 'plyr', 'progress'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Packages suggested but not available for checking: 'LIM', 'sybil'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'abc.data', 'quantreg', 'locfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'matrixStats', 'ranger', 'doParallel', 'foreach', 'stringr',
  'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'abc', 'abind', 'plyr', 'Hmisc'

Packages suggested but not available for checking: 'ggplot2', 'abc.data'

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

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

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', 'plyr', 'HH', 'ICC', 'vcd', 'Hmisc'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'text'
multiplot: no visible global function definition for 'lines'
multiplot: no visible global function definition for 'par'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
Undefined global functions or variables:
  abline lines par rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "text")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'purrr', 'rlang', 'rstudioapi', 'stringi',
  'stringr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'lme4', 'Rgraphviz', 'rjags', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'INLA', 'knitr', 'R.rsp', 'testthat', 'entropy', 'moments', 'brglm'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'ggplot2', 'gridExtra', 'colourpicker', 'shinythemes',
  'emojifont', 'rintrojs'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'mvtnorm', 'sn', 'qgam', 'truncnorm', 'plotrix',
  'RColorBrewer'

Package suggested but not available for checking: 'testthat'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pander'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mhsmm', 'zoo', 'PhysicalActivity', 'nleqslv', 'plyr', 'DBI',
  'RSQLite', 'circlize', 'ggplot2', 'R.utils', 'iterators', 'Rcpp',
  'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tcltk2', 'fgui', 'SMPracticals'

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

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: 'optimx', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for 'pchisq'
print.linML: no visible global function definition for 'pchisq'
print.loglinML: no visible global function definition for 'pchisq'
print.satMarML: no visible global function definition for 'pchisq'
print.satMcarWLS: no visible global function definition for 'pchisq'
summary.funlinWLS: no visible global function definition for 'pchisq'
summary.linML: no visible global function definition for 'pchisq'
summary.loglinML: no visible global function definition for 'pchisq'
summary.satMarML: no visible global function definition for 'pchisq'
summary.satMcarWLS: no visible global function definition for 'pchisq'
summary.waldTest: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package required but not available: 'stringr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lhs', 'Rcpp', 'compare', 'randtoolbox', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'htmlwidgets', 'reactR', 'rstudioapi'

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
Packages required but not available: 'httr', 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gamlss', 'gamlss.dist', 'Hmisc'

Package suggested but not available for checking: 'ineq'

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

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: 'knitr', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'aroma.affymetrix', 'R.methodsS3', 'R.oo', 'R.utils', 'matrixStats',
  'R.filesets', 'aroma.core'

Package suggested but not available for checking: 'DNAcopy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'R.utils', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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 suggested but not available for checking: 'mvtnorm'
Packages required but not available: 'tuneR', 'zoo', 'seewave'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dummies', 'randomForest', 'kernelFactory', 'ada'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'R.utils', 'dplyr', 'purrr', 'readr', 'stringr',
  'hunspell'

Package suggested but not available for checking: 'testthat'

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

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

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', 'XML', 'plyr', 'httr'

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

Package suggested but not available for checking: 'effects'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R.methodsS3', 'GDINA'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'circular', 'data.table', 'DiagrammeR', 'DiagrammeRsvg', 'fasttime',
  'ggplot2', 'svglite', 'knitr', 'readr', 'reshape2', 'rmarkdown',
  'rsvg', 'scales', 'stringr', 'stringi'

Packages suggested but not available for checking:
  'raster', 'gdistance', 'sp', 'rgdal', 'testthat', 'RGtk2',
  'gWidgets2RGtk2', 'gWidgets2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geosphere', 'ggmap', 'glue', 'httr', 'lubridate',
  'magrittr', 'rlang', 'tibble', 'timetk', 'xml2'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19', 'Biostrings',
  'GenomeInfoDb', 'GenomicRanges', 'IRanges', 'S4Vectors'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'hetGP', 'lhs', 'numDeriv', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'metap', 'EmpiricalBrownsMethod'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mclust', 'runjags', 'circular', 'overlap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'matrixStats', 'data.table', 'R.utils'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'stringi', 'textutils', 'progress', 'XML', 'xml2',
  'openxlsx'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'RProtoBuf', 'Rserve', 'RestRserve', 'yaml'

Packages suggested but not available for checking:
  'randomForest', 'testthat', 'callr'

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

Package suggested but not available for checking: 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Anthropometry', 'archetypes', 'FNN', 'foreach', 'nnls', 'tolerance',
  'univOutl'

Packages suggested but not available for checking: 'doParallel', 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'imputeYn', 'glmnet', 'lars', 'quadprog'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'speedglm', 'xgboost', 'doParallel', 'foreach'

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

Packages suggested but not available for checking:
  'devtools', 'git2r', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'shiny', 'pracma', 'DataVisualizations'

Packages suggested but not available for checking:
  'mclust', 'foreach', 'dqrng', 'parallelDist', 'knitr', 'rmarkdown',
  'reshape2', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'glmnet', 'HDtweedie', 'testthat', 'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'glmnet'
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:
  'coda', 'mvtnorm', 'MCMCpack', 'spatstat'

Depends: includes the non-default packages:
  'Matrix', 'coda', 'mvtnorm', 'MCMCpack', 'spatstat', 'parallel'
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:
  'missForest', 'e1071', 'WGCNA', 'ComICS', 'pheatmap', 'doParallel',
  'quantmod', 'preprocessCore', 'pcaMethods', 'foreach', 'nnls',
  'ranger'

Packages suggested but not available for checking: 'R.rsp', 'DeconRNASeq'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: 'caret', 'e1071'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'clinfun', 'gsDesign'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'rmarkdown', 'rvest', 'xml2'

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

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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mtukey.test : p.test: no visible global function definition for 'qf'
mtukey.test: no visible binding for global variable 'quantile'
mtukey.test: no visible global function definition for 'rnorm'
tukey.test: no visible global function definition for 'qf'
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
Packages required but not available: 'combinat', 'glm2', 'turboEM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'spdep', 'splancs', 'waveslim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'adegraphics'

Packages suggested but not available for checking: 'pixmap', 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'igraph', 'ape', 'shiny', 'ggplot2', 'seqinr', 'spdep',
  'reshape2', 'dplyr', 'vegan'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
  'maptools', 'tkrplot', 'rgeos'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking: 'maptools', 'tkrplot'

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

Packages suggested but not available for checking: 'maptools', 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'phylobase', 'ape', 'adegenet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'audio', 'shape', 'Cairo', 'dplyr', 'readr', 'rlang', 'tidyr',
  'haven', 'shinyWidgets', 'gclus', 'TeachingDemos'

Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'gridExtra', 'spelling', 'adeptdata', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'
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Packages suggested but not available for checking: 'testthat', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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VignetteBuilder packages required for checking but not installed:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'shinyWidgets', 'shinyjs', 'V8', 'colourpicker', 'viridisLite',
  'highlight', 'clipr', 'knitr', 'readODS', 'readxl', 'haven', 'DBI',
  'RMariaDB', 'RSQLite', 'scales', 'rsvg'

Packages suggested but not available for checking: 'rmarkdown', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'adegraphics', 'adephylo', 'ape', 'phylobase', 'phytools',
  'rgl', 'FactoMineR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'BiocGenerics'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package unavailable to check Rd xrefs: 'QCA'
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Package suggested but not available for checking: 'coda'

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

Packages suggested but not available for checking:
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  'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'Rdpack', 'doParallel', 'foreach', 'RcppArmadillo'

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

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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VignetteBuilder package required for checking but not installed: 'knitr'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'httr', 'tidyr', 'rlang', 'lubridate', 'ggplot2', 'scales',
  'lifecycle', 'glue', 'tibble', 'knitr'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
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  'dplyr', 'ggplot2', 'tidyr', 'gridExtra', 'bookdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'spatstat.geom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'purrr', 'dplyr', 'magrittr', 'assertthat', 'mvtnorm', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'pryr', 'MCMCpack'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'knitr', 'clue', 'ggplot2', 'reshape2'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'learnr', 'BayesFactor', 'dplyr', 'car', 'effsize', 'effects',
  'forcats', 'GGally', 'ggplot2', 'Hmisc', 'lm.beta', 'readr',
  'robust', 'sandwich', 'sjstats', 'tidyr', 'WRS2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'writexl', 'ggvis', 'lubridate', 'plotly', 'ggplot2',
  'tidyr', 'circular', 'scales', 'zoo', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'lmtest', 'sandwich', 'zoo', 'Formula'

Packages suggested but not available for checking:
  'dynlm', 'effects', 'fGarch', 'forecast', 'ineq', 'longmemo',
  'mlogit', 'np', 'plm', 'pscl', 'quantreg', 'rgl', 'ROCR', 'rugarch',
  'sampleSelection', 'scatterplot3d', 'strucchange', 'systemfit',
  'truncreg', 'tseries', 'urca', 'vars'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'pbkrtest', 'lmerTest', 'car', 'reshape2'

Packages suggested but not available for checking:
  'emmeans', 'coin', 'xtable', 'plyr', 'optimx', 'nloptr', 'knitr',
  'rmarkdown', 'R.rsp', 'latticeExtra', 'multcomp', 'testthat',
  'mlmRev', 'dplyr', 'tidyr', 'dfoptim', 'psychTools', 'ggplot2',
  'MEMSS', 'effects', 'carData', 'ggbeeswarm', 'cowplot', 'jtools',
  'ggpubr', 'ggpol', 'glmmTMB', 'brms', 'rstanarm', 'statmod',
  'ggResidpanel'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'expm', '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:
  'reshape2', 'mvtnorm', 'ggplot2', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'stringr', 'gstat', 'fractaldim', 'rgl', 'pracma',
  'gridExtra', 'moments', 'ggplot2', 'sp', 'png', 'plyr', 'igraph',
  'shiny', 'shinyjs', 'scales', 'dbscan', 'mixtools', 'fftwtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'minpack.lm', 'gridExtra', 'scales', 'dplyr', 'DBI',
  'assertthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'drgee', 'stdReg', 'data.table', 'ivtools'

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

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvQuad', 'matrixStats', 'stringr', 'magrittr', 'dplyr', 'tidyr',
  'tidyselect', 'rlang', 'polynom', 'tibble', 'purrr'

Packages suggested but not available for checking:
  'trustOptim', 'trust', 'numDeriv', 'testthat', 'knitr', 'rmarkdown',
  'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'anytime', 'binaryLogic', 'data.table', 'DescTools', 'dplyr', 'GGIR',
  'lubridate', 'magrittr', 'PAutilities', 'rlang', 'reshape2',
  'seewave', 'stringr', 'Rcpp'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: 'testthat', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'miscF', 'lme4', 'R2jags', 'coda'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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  'AER', 'agricolae', 'betareg', 'broom', 'car', 'coin', 'corrgram',
  'desplot', 'dplyr', 'effects', 'equivalence', 'emmeans', 'FrF2',
  'gam', 'gge', 'ggplot2', 'gnm', 'gstat', 'HH', 'knitr',
  'latticeExtra', 'lme4', 'lucid', 'mapproj', 'maps', 'MCMCglmm',
  'metafor', 'NADA', 'nullabor', 'ordinal', 'pbkrtest', 'pls', 'pscl',
  'reshape2', 'rgdal', 'rmarkdown', 'qicharts', 'qtl', 'sp', 'SpATS',
  'vcd', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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
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:
  'lmerTest', 'emmeans', 'pbkrtest', 'ggplot2'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgeos'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gtable', 'plyr', 'zoo', 'abind', 'raster', 'ggpubr',
  'cowplot', 'reshape', 'ggforce', 'ncdf4', 'easyNCDF', 'sp',
  'multiApply'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotrix', 'raster', 'sp', 'RandomFields', 'coda', 'unmarked',
  'mvtnorm', 'spdep'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'partitions'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixcalc', 'pracma', 'purrr', 'pdist', 'ggplot2', 'visNetwork',
  'magrittr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'Biostrings', 'microbenchmark', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rdpack', 'magrittr', 'knitr', 'tidyr', 'dplyr', 'randomNames'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rscala', 'commonsMath'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'betareg', 'coxme', 'fitdistrplus', 'glmmTMB', 'lavaan', 'lme4',
  'maxlike', 'ordinal', 'pscl', 'R2jags', 'R2OpenBUGS', 'R2WinBUGS',
  'jagsUI', 'lmerTest'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tseries', 'nortest', 'ggplot2', 'psych', 'meta', 'stringr'

Package suggested but not available for checking: 'onewaytests'

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

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', 'rgl', 'magrittr'

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

Package suggested but not available for checking: 'gridExtra'

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:
  'lubridate', 'dplyr', 'rvest', 'tidyr', 'stringr', 'xml2', 'httr',
  'readr', 'sp', 'progress', 'readxl'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'ggseas', 'mapproj',
  'selectr', 'covr', 'ggmap'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'caRamel', 'coda', 'DEoptim', 'dplyr', 'FME',
  'ggmcmc', 'hydroPSO', 'imputeTS', 'Rmalschains', 'GGally', 'ggplot2',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'airGR', 'dygraphs', 'markdown', 'plotrix', 'shiny', 'shinyjs', 'xts'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'htmlwidgets'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'reshape2', 'tibble'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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: 'tibble'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'countrycode', 'cowplot', 'dplyr', 'dygraphs', 'geodist',
  'geosphere', 'GGally', 'ggmap', 'ggplot2', 'gridExtra', 'httpcode',
  'httr', 'jsonlite', 'leaflet', 'lubridate', 'magrittr',
  'MazamaCoreUtils', 'MazamaLocationUtils', 'MazamaSpatialUtils',
  'openair', 'PWFSLSmoke', 'readr', 'RColorBrewer', 'rlang', 'scales',
  'seismicRoll', 'sp', 'stringr', 'tibble', 'tidyr', 'tidyselect',
  'worldmet', 'xts', 'zoo'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'V8', 'yaml', 'RJSONIO'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dke.fun.default: no visible global function definition for 'hist'
kef: no visible global function definition for 'dbinom'
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
plot.dke.fun: no visible global function definition for 'hist'
plot.dke.fun: no visible global function definition for 'lines'
plot.hcvc.fun1d: no visible global function definition for
  'plot.default'
plot.hcvd.fun1d: no visible global function definition for
  'plot.default'
plot.kern.fun1d: no visible global function definition for
  'plot.default'
plot.kpmfe.fun1d: no visible global function definition for
  'plot.default'
plot.reg.fun1d: no visible global function definition for
  'plot.default'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
Packages required but not available: 'dplyr', 'data.table', 'zoo', 'shiny'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
Packages required but not available:
  'kml', 'dplyr', 'signal', 'Hmisc', 'ggplot2', 'clusterCrit'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'digest', 'gdtools', 'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'data.table', 'digest', 'httr', 'jsonlite', 'sp',
  'stringr', 'wellknown'

Packages suggested but not available for checking:
  'ape', 'covr', 'dplyr', 'ggplot2', 'jpeg', 'knitr', 'mapdata',
  'maps', 'maptools', 'phytools', 'rmarkdown', 'testthat', 'tidyr',
  'vegan'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'airr', 'ape', 'Biostrings', 'dplyr', 'GenomicAlignments',
  'igraph', 'IRanges', 'lazyeval', 'progress', 'Rcpp', 'readr',
  'rlang', 'scales', 'seqinr', 'stringi', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages which this enhances but not available for checking: 'eemR', 'EEM'

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

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

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'plyr', 'caret', 'seqinr', 'randomForest', 'ROCR',
  'reshape2', 'bio3d'

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', 'magrittr', 'lubridate', 'jsonlite',
  'rlang', 'curl'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'magrittr', 'stringr'

Packages suggested but not available for checking:
  'devtools', 'httptest', 'roxygen2', 'testthat', 'knitr', 'rmarkdown',
  'covr', 'remotes', 'spelling', 'fs'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'lubridate', 'plyr', 'RCurl', 'rvest', 'taxize', 'XML',
  'xml2'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'base64enc', 'httr', 'rjson'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'RUnit'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'limma', 'org.Hs.eg.db', 'AnnotationDbi', 'foreach',
  'readr', 'RCurl'

Package suggested but not available for checking: 'spelling'

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

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'clipr', 'ghql', 'git2r', 'httr', 'jsonlite', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'webmockr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/alleHap.Rnw'
(Is a VignetteBuilder field missing?)

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

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pedigree'
Packages required but not available: 'vegan', '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', 'speedglm', 'tidyr', 'stringr', 'dplyr'

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
batch.possSpells.fnc: no visible binding for global variable 'words'
possSpells.fnc: no visible binding for global variable 'len.phons'
possSpells.fnc: no visible binding for global variable 'phon1'
possSpells.fnc: no visible binding for global variable 'len.total'
possSpells.fnc: no visible binding for global variable 'poss.spells'
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Skipping vignette re-building
Packages suggested but not available for checking:
  'devtools', 'testthat', 'reshape2', 'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'
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
Packages required but not available:
  'glue', 'lubridate', 'magrittr', 'R6', 'rlang', 'V8', 'vctrs'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'randomForest', 'caTools', 'cli', 'dlookr', 'dplyr',
  'future', 'ggmosaic', 'MLmetrics', 'party', 'purrr', 'ROCR',
  'ranger', 'rlang', 'tibble', 'tidyr', 'tidyselect', 'unbalanced',
  'xgboost'

Packages suggested but not available for checking:
  'knitr', 'ISLR', 'mice', 'mlbench'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'Formula', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bife', 'car', 'knitr', 'lfe', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tripack', 'R.utils', 'sgeostat', 'spatstat', 'splancs'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'directlabels', 'gdata', 'ggplot2', 'pedigree', 'Rcpp', 'reshape'

Packages suggested but not available for checking:
  'RColorBrewer', 'truncnorm', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'alphahull'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'Rcpp', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'fBasics', 'FMStable', 'RUnit', 'Rmpfr', 'sfsmisc'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'glue', 'httr', 'jsonlite', 'purrr', 'readr', 'stringr',
  'tibble', 'tidyr', 'timetk'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Packages required but not available: 'leaps', 'SuppDists', 'car'

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

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

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:
  'reticulate', 'htmlwidgets', 'assertthat', 'magrittr', 'vegawidget',
  'repr'

Packages suggested but not available for checking:
  'httr', 'rprojroot', 'purrr', 'readr', 'knitr', 'rmarkdown',
  'tibble', 'listviewer', 'testthat', 'pryr', 'stringr', 'tidyr',
  'dplyr', 'pkgdown', 'processx', 'rsvg', 'png', 'fs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'purrr', 'lubridate', 'dplyr', 'magrittr',
  'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rjags', 'coda', 'lme4', 'metafor'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'magrittr', 'sjmisc', 'xml2', 'data.table',
  'furrr'

Packages suggested but not available for checking:
  'stringr', 'knitr', 'rmarkdown', 'testthat', 'spelling', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Biobase'
Malformed Description field: should contain one or more complete sentences.
EXP.step: no visible global function definition for 'rgamma'
EXP.step: no visible global function definition for 'rnorm'
MAX.step: no visible global function definition for 'uniroot'
Norm.GMedian: no visible binding for global variable 'median'
RNASeq.Data.Gene: no visible binding for global variable 'quantile'
decom.initial: no visible global function definition for 'kmeans'
decom.initial: no visible global function definition for 'quantile'
decom.initial: no visible global function definition for 'var'
dispersion.nb.QL: no visible binding for global variable 'quantile'
est.mu.nb.mle: no visible global function definition for 'runif'
est.v.nb.QL: no visible global function definition for 'runif'
pdf2grid: no visible global function definition for 'dnorm'
pdf2grid: no visible global function definition for 'dgamma'
prior.grid: no visible global function definition for 'sd'
prior.grid: no visible global function definition for 'dnorm'
test.AMAP: no visible global function definition for 'rgamma'
test.AMAP: no visible global function definition for 'rnorm'
test.AMAP: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Packages required but not available:
  'classInt', 'doParallel', 'foreach', 'Hmisc', 'latex2exp', 'ncdf4',
  'raster', 'rgdal', 'rgeos', 'scico', 'sp', 'viridis', 'xtable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fs', 'log', 'cli', 'glue', 'here', 'httpuv', 'promises', 'jsonlite',
  'websocket', 'assertthat'

Packages suggested but not available for checking:
  'mime', 'readr', 'htmltools', 'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'Zelig'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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
Skipping vignette re-building
Packages suggested but not available for checking:
  'coda', 'network', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'magrittr'

Package suggested but not available for checking: 'covr'

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

Packages suggested but not available for checking:
  'ProTrackR', 'adfExplorer'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'agricolae', 'ggcorrplot', 'ggplot2', 'reshape2', 'Rdpack',
  'mathjaxr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pander', 'XML', 'httr', 'RCurl'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'R.rsp', 'shiny', 'shinyBS', 'knitr', 'AICcmodavg'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking: 'maptools', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'biogram', 'devtools', 'pbapply', 'ranger', 'shiny', 'stringi'

Packages suggested but not available for checking:
  'DT', 'ggplot2', 'pander', 'rmarkdown', 'shinythemes', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Peptides', 'caret', 'kernlab', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'e1071'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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', 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
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  'pillar', 'readxl', 'rmarkdown', 'rstudioapi', 'rvest', 'skimr',
  'testthat', 'tidyr', 'xml2'

VignetteBuilder packages required for checking but not installed:
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Packages unavailable to check Rd xrefs: 'dplyr', 'ggplot2'
Packages required but not available:
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  'lubridate', 'magrittr', 'purrr', 'raster', 'Rdpack', 'Rcpp',
  'rgeos', 'rlang', 'sf', 'sp', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'adehabitatLT', 'adehabitatMA', 'broom', 'ggplot2', 'ggraph',
  'geosphere', 'FNN', 'bcpa', 'leaflet', 'moveHMM', 'move',
  'sessioninfo', 'spacetime', 'trajectories', 'knitr', 'rmarkdown',
  'tinytest', 'tidygraph', 'maptools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'biogram', 'ranger', 'seqinr', 'shiny'

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

Packages suggested but not available for checking:
  'knitr', 'Hmisc', 'coda', 'testthat', 'lmodel2', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'magrittr', 'yaml'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ssh', 'aws.s3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'vegan3d', 'analogue', 'rgl'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'pipeR', 'ggplot2', 'dplyr', 'futile.logger', 'RCurl',
  'rlang', 'proto', 'purrr'

Packages suggested but not available for checking:
  'plotly', 'knitr', 'rmarkdown', 'visNetwork', 'rjson', 'DT', 'shiny',
  'R.devices', 'corrplot', 'car'

Packages which this enhances but not available for checking:
  'SparkR', 'reticulate'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'tkrplot'

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

Packages suggested but not available for checking:
  'data.table', 'testthat', 'tidyr', 'reshape2', 'rmarkdown', 'shiny',
  'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Analyz.loadSteps,Analyz: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package required but not available: 'svd'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for 'plot.new'
andrews: no visible global function definition for 'plot.window'
andrews: no visible global function definition for 'title'
andrews: no visible global function definition for 'axis'
andrews: no visible global function definition for 'box'
andrews: no visible global function definition for 'lines'
andrews: no visible global function definition for 'rainbow'
andrews: no visible global function definition for 'hsv'
selectand: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'RSQLite', 'DBI', 'zip', 'dbplyr', 'tidyselect', 'cli',
  'rlang', 'pillar'

Packages suggested but not available for checking:
  'testthat', 'stringr', 'knitr', 'rmarkdown', 'tibble', 'rJava'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'extrafont', 'dplyr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'nabor', 'ncdf4', 'proj4', 'sp', 'spbabel'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'brms', 'circular', 'overlap', 'loo', 'ggplot2', 'gridExtra',
  'activityGCMM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'maptools', 'sp', 'rgeos', 'MCMCpack', 'ellipse', 'mvtnorm',
  'deldir', 'colorspace', 'png', 'bezier', 'HDInterval', 'plyr',
  'ggplot2', 'rgdal'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'maptools', 'zoo', 'forcats', 'lubridate', 'tibble',
  'shinyBS', 'shinyjs', 'shiny', 'shinyWidgets', 'shinycssloaders',
  'shinythemes', 'leaflet', 'leaflet.extras', 'dplyr', 'ggplot2',
  'scales', 'tidyr', 'sp', 'rgdal', 'raster', 'geosphere'

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

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

Package suggested but not available for checking: 'testit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'RJSONIO', 'gtable', 'plyr', 'reshape2', 'scales',
  'tibble', 'lazyeval', 'knitr'

Packages suggested but not available for checking:
  'servr', 'gistr', 'shiny', 'htmltools', 'rmarkdown', 'testthat',
  'devtools', 'httr', 'maps', 'ggplot2movies', 'hexbin', 'Hmisc',
  'mapproj', 'maptools', 'quantreg', 'svglite'

Package which this enhances but not available for checking: 'sp'

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

Packages suggested but not available for checking:
  'maps', 'knitr', 'mapdata', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'animation', 'RColorBrewer', 'scales', 'sp', 'raster', 'ggmap'

Packages suggested but not available for checking:
  'ellipse', 'igraph', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'shiny'

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

Packages suggested but not available for checking:
  'DiceKriging', 'TruncatedNormal', 'tmg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'reshape2', 'ggplot2', 'viridisLite', 'RcppArmadillo',
  '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: 'assertthat', 'R6', 'reticulate'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
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.
Packages required but not available:
  'mc2d', 'tseries', 'EnvStats', 'fitdistrplus', 'actuar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'igraph'
Packages required but not available:
  'dplyr', 'glue', 'timetk', 'sweep', 'tibbletime', 'purrr', 'rlang',
  'tibble', 'tidyr', 'ggplot2', 'cli', 'crayon', 'rstudioapi'

Packages suggested but not available for checking:
  'tidyverse', 'tidyquant', 'stringr', 'testthat', 'covr', 'knitr',
  'rmarkdown', 'devtools', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rlang', 'assertive', 'Rdpack', 'ggplot2', 'reshape2',
  'Rcpp', 'robustbase', 'cowplot', 'BH'

Package suggested but not available for checking: 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'wnominate', 'pscl', 'MCMCpack'

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

Packages suggested but not available for checking:
  'knitr', 'lme4', 'sandwich'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/ANOM.Rnw'
(Is a VignetteBuilder field missing?)

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'rhandsontable', 'DescTools', 'HH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'rhandsontable', 'DescTools', 'HH'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'datasauRus', 'maps', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'maps'
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: 'caret', 'rJava', 'RWeka'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'antaresRead', 'assertthat', 'data.table', 'whisker'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'rhdf5', 'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'bit64', 'lubridate', 'plyr', 'stringr', 'shiny'

Packages suggested but not available for checking:
  'rhdf5', 'testthat', 'covr', 'knitr', 'rmarkdown', 'foreach', 'DT',
  'htmltools', 'antaresEditObject'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'antaresRead', 'antaresProcessing', 'spMaps', 'dygraphs', 'shiny',
  'plotly', 'htmltools', 'htmlwidgets', 'manipulateWidget', 'leaflet',
  'sp', 'rgeos', 'raster', 'webshot', 'data.table', 'lubridate',
  'geojsonio', 'leaflet.minicharts', 'assertthat', 'rAmCharts'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rhdf5', 'ggplot2', 'hexbin', 'knitr',
  'visNetwork', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotrix', 'scatterplot3d', 'shiny', 'smacof'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shapes', 'rgl', 'archetypes', 'nnls', 'depth', 'FNN', 'ICGE',
  'biclust'

Packages suggested but not available for checking:
  'knitr', 'calibrate', 'mvtnorm', 'SportsAnalytics', 'RColorBrewer',
  'plotrix', 'abind'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Anthropometry.Rnw'
(Is a VignetteBuilder field missing?)

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'knitr', 'Rglpk', 'rmarkdown', 'testthat'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'ggplot2', 'bookdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjson', 'plyr', 'assertthat', 'httr', 'leafletR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'glue', 'purrr', 'config', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'withr', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'dplyr', 'readr', 'lubridate', 'vroom', 'glue', 'purrr',
  'stringr', 'curl', 'usethis', 'roxygen2', 'progress'

Packages suggested but not available for checking:
  'testthat', 'nycflights13', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'withr', 'BiocManager', 'httr', 'curl'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'tinytest', 'gettz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'lme4'
'library' or 'require' call to 'boot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for 'boot'
Undefined global functions or variables:
  boot
Packages unavailable to check Rd xrefs: 'lme4', 'geepack', 'dispmod'
Running examples in 'aod-Ex.R' failed
The error most likely occurred in:

> ### Name: iccbin
> ### Title: Intra-Cluster Correlation for Binomial Data
> ### Aliases: iccbin show,iccbin-method
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> data(rats)
> tmp <- rats[rats$group == "TREAT", ]
> # A: glmm (model linearization)
> iccbin(n, y, data = tmp, method = "A")
Error in loadNamespace(x) : there is no package called 'lme4'
Calls: iccbin ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'lme4'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'roxygen2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rbenchmark', 'R6', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'data.table', 'httr', 'sf'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'knitr', 'magrittr', 'mapview',
  'rmarkdown', 'scales', 'testthat', 'units'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Package suggested but not available for checking: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cellranger', 'purrr', 'data.table', 'lazyeval'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'afex', 'ez', 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'haven', 'survey', 'magrittr', 'tidyverse', 'dplyr', 'ggplot2',
  'data.table', 'ggpubr', 'stringr'

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

Packages suggested but not available for checking:
  'Biostrings', 'kebabs', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/apcluster.Rnw'
(Is a VignetteBuilder field missing?)

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'reshape', 'plm', 'survey', 'lmtest', 'car', 'ISLR', 'AER',
  'ggplot2', 'ChainLadder'

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

Packages suggested but not available for checking: 'gee', 'expm', 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'htmlwidgets', 'magrittr', 'rlang', 'ggplot2', 'jsonlite', 'shiny'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'htmltools', 'shinymaterial', 'shinyjs', 'rhandsontable',
  'rmarkdown', 'ggraph', 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
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(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/aplore3-examples.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'ggplot2', 'patchwork', 'magrittr'

Packages suggested but not available for checking: 'rvcheck', 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tkrplot', 'jpeg', 'png'
Packages required but not available: 'Rcpp', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'Deriv', 'matrixStats', 'RSGHB', 'coda', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'rvest', 'glue', 'xml2', 'lubridate'

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', 'rlang', 'glue', 'tibble', 'proxyC', 'dplyr',
  'purrr', 'tidyselect', 'tidyr'

Packages suggested but not available for checking:
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  'spelling', 'xml2', 'modeldata'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'emulator', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'optmatch'
Packages required but not available:
  'logistf', 'penalized', 'rms', 'shrink'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

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.
Malformed Description field: should contain one or more complete sentences.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for 'write.table'
runAPSIM: no visible global function definition for 'read.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'DBI', 'jsonlite', 'knitr', 'RSQLite', 'xml2'

Packages suggested but not available for checking:
  'BayesianTools', 'FedData', 'ggplot2', 'GSODR', 'listviewer',
  'mvtnorm', 'nasapower', 'nloptr', 'raster', 'reactR', 'rmarkdown',
  'sp', 'spData', 'sf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages unavailable to check Rd xrefs: 'AER', 'gee', 'survey'
Packages required but not available:
  'ape', 'brranching', 'phytools', 'taxize', 'xml2'

Packages suggested but not available for checking:
  'paco', 'vegan', 'knitr', 'rmarkdown', 'qpdf'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'quantreg', 'cubature', 'coda', 'pbapply'

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

Packages suggested but not available for checking:
  'testthat', 'survey', 'srvyr', 'vdiffr', 'covr', 'outbreaks',
  'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Packages required but not available: 'plyr', 'sp', 'stringr', 'data.table'

Packages suggested but not available for checking:
  'colorspace', 'ape', 'soilDB', 'latticeExtra', 'tactile',
  'compositions', 'sharpshootR', 'markovchain', 'xtable', 'testthat',
  'Gmedian', 'farver', 'Hmisc', 'tibble', 'RColorBrewer', 'scales',
  'digest', 'mpspline2', 'soiltexture', 'gower'

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

Packages suggested but not available for checking:
  'rgeos', 'rgdal', 'knitr', 'devtools', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'deSolve'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 1 marked UTF-8 string
Packages required but not available:
  'mvtnorm', 'tmvtnorm', 'msm', 'numDeriv'

Package suggested but not available for checking: 'SMNCensReg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'rjags', 'ArchaeoPhases', 'Bchron'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'hdrcde', 'shiny', 'shinythemes', 'DT', 'readr', 'ggthemes',
  'toOrdinal', 'ggplot2', 'ggalt', 'reshape2', 'dplyr', 'digest',
  'gplots', 'magrittr', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ArchaeoPhases.dataset'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ca', 'circular', 'plotrix', 'spatstat'
Note: found 76 marked Latin-1 strings
Packages required but not available: 'RBGL', 'igraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'here', 'knitr', 'log4r', 'config', 'tidyverse', 'rmarkdown',
  'skimr', 'stringr', 'snakecase', 'testthat', 'bannerCommenter',
  'feather', 'readr', 'ps'

Packages suggested but not available for checking:
  'RCurl', 'broom', 'caret', 'covr', 'gtsummary', 'performance',
  'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'vcd', 'mlbench', 'ggplot2', 'TSP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'XML', 'geometry', 'sp'

Packages suggested but not available for checking: 'rgl', 'TDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'plyr', 'rgl', 'lidR', 'FNN', 'DiceKriging',
  'circular', 'pkgcond', 'stringr', 'progress', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'anytime', 'dplyr', 'ggplot2', 'gridExtra', 'httr', 'jsonlite',
  'lubridate', 'rvest', 'stringr', 'tibble', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'vcr', 'webmockr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'archivist', 'httr', 'git2r', 'jsonlite', 'digest'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RCurl', 'digest', 'httr', 'DBI', 'lubridate', 'RSQLite', 'magrittr',
  'flock'

Packages suggested but not available for checking:
  'shiny', 'dplyr', 'testthat', 'ggplot2', 'devtools', 'knitr',
  'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'magrittr', 'jsonlite', 'dplyr', 'tidyr', 'urltools',
  'httr', 'curl', 'vroom'

Packages suggested but not available for checking:
  'ggplot2', 'forcats', 'leaflet', 'knitr', 'sf', 'tigris', 'testthat',
  'rmarkdown', 'data.table', 'formattable', 'geofacet', 'lubridate',
  'scales', 'viridis', 'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'qCBA'

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

Packages suggested but not available for checking:
  'testthat', 'data.table', 'dplyr', 'knitr', 'rmarkdown', 'ggplot2',
  'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for 'filter'
ardec.lm: no visible global function definition for 'ar'
ardec.lm: no visible global function definition for 'lm'
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
Packages required but not available:
  'aod', 'dplyr', 'dynlm', 'lmtest', 'msm', 'stringr', 'zoo'

Packages suggested but not available for checking:
  'qpcR', 'sandwich', 'xts'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'dplyr', 'magrittr', 'readr', 'rlang', 'sf', 'stringr',
  'tibble', 'tidyr', 'tidyselect', 'tabshiftr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'tidyr', 'magrittr', 'dplyr', 'purrr', 'shiny',
  'shinydashboard', 'shinyBS', 'shinyjs', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ingredients', 'iBreakDown', 'gistr', 'jsonlite', 'plumber',
  'auditor', 'DALEX', 'fairmodels'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr', 'pkgdown', 'covr',
  'ranger'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Package suggested but not available for checking: 'magrittr'

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

Packages suggested but not available for checking:
  'magrittr', 'knitr', 'rmarkdown', 'shiny'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xts', 'glmnet', 'zoo', 'XML', 'xtable'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'findpython', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'hommel', 'RNifti', 'plyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'httr', 'ari', 'rmarkdown', 'pdftools', 'rvest', 'magrittr',
  'mime', 'jsonlite', 'text2speech', 'docxtractr', 'tuneR', 'yaml'

Packages suggested but not available for checking:
  'knitr', 'covr', 'testthat', 'pagedown', 'webshot', 'rstudioapi',
  'base64enc', 'xaringan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'text2speech', 'tuneR', 'webshot', 'purrr', 'rmarkdown', 'xml2',
  'rvest', 'progress', 'hms'

Packages suggested but not available for checking:
  'testthat', 'xaringan', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'R.utils', 'progress', 'readr', 'spelling', 'dplyr', 'dbplyr',
  'nycflights13', 'testthat', 'knitr', 'covr', 'fs', 'rmarkdown',
  'RSQLite', 'duckdb', 'vroom', 'utf8', 'MonetDBLite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'mvtnorm', 'ClustOfVar', 'FAMT', 'VSURF', 'glmnet', 'anapuce',
  'qvalue', 'doParallel', 'impute', 'ComplexHeatmap', 'circlize'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'abind', 'coda', 'Hmisc'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'np', 'Hmisc', 'moments', 'nor1mix', 'spatstat.geom', 'spatstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.utils', 'aroma.core', 'R.methodsS3', 'R.oo', 'R.cache',
  'R.devices', 'R.filesets', 'aroma.apd', 'matrixStats', 'listenv',
  'future'

Packages suggested but not available for checking:
  'DBI', 'gsmoothr', 'RColorBrewer', 'Biobase', 'BiocGenerics',
  'affxparser', 'affy', 'affyPLM', 'aroma.light', 'gcrma', 'limma',
  'oligo', 'oligoClasses', 'pdInfoBuilder', 'preprocessCore',
  'AffymetrixDataTestFiles', 'dChipIO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.methodsS3', 'R.oo', 'R.utils', 'R.huge'

Package suggested but not available for checking: 'affxparser'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.utils', 'aroma.core', 'R.methodsS3', 'R.oo', 'R.filesets',
  'R.cache', 'matrixStats', 'PSCBS'

Packages suggested but not available for checking:
  'aroma.light', 'DNAcopy', 'GLAD'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.utils', 'R.filesets', 'R.devices', 'R.methodsS3', 'R.oo',
  'R.cache', 'R.rsp', 'matrixStats', 'RColorBrewer', 'PSCBS',
  'listenv', 'future', 'BiocManager'

Packages suggested but not available for checking:
  'png', 'Cairo', 'EBImage', 'preprocessCore', 'aroma.light',
  'DNAcopy', 'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'alphashape3d', 'compositions', 'doParallel', 'foreach',
  'geometry', 'Morpho', 'rgl', 'Rvcg', 'stringr', 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gmm', 'sandwich', 'mvtnorm', 'tmvtnorm', 'numDeriv', 'lmec',
  'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'shiny', 'plyr', 'reshape2', 'dplyr', 'ggplot2', 'viridis', 'knitr',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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
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: 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gmp', 'R6'

Packages suggested but not available for checking:
  'foreach', 'knitr', 'rmarkdown', 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'bit64', 'purrr', 'R6', 'rlang', 'tidyselect', 'vctrs',
  'cpp11'

Packages suggested but not available for checking:
  'decor', 'distro', 'dplyr', 'hms', 'knitr', 'lubridate', 'pkgload',
  'reticulate', 'rmarkdown', 'testthat', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'broom', 'magrittr', 'rmarkdown', 'testthat', 'xtable', 'pander',
  'coin', 'pROC', 'yaml', 'geepack'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'car', 'plyr', 'magrittr', 'dplyr', 'emmeans'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'tidyr', 'pander',
  'lmerTest', 'phia', 'psych', 'stringi', 'DescTools', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package which this enhances but not available for checking: 'ARTP'

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 required but not available: 'arules', 'discretization', 'glmnet'

Packages suggested but not available for checking:
  'testthat', 'RWeka', 'rJava'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'pmml', 'XML', 'arulesViz', 'arulesCBA', 'testthat'
Packages unavailable to check Rd xrefs: 'arulesCBA', 'pmml'
Running examples in 'arules-Ex.R' failed
The error most likely occurred in:

> ### Name: read.PMML
> ### Title: Read and Write PMML
> ### Aliases: read.PMML write.PMML
> ### Keywords: interface
> 
> ### ** Examples
> 
> data("Groceries")
> 
> rules <- apriori(Groceries, parameter=list(support=0.001))
Apriori

Parameter specification:
 confidence minval smax arem  aval originalSupport maxtime support minlen
        0.8    0.1    1 none FALSE            TRUE       5   0.001      1
 maxlen target  ext
     10  rules TRUE

Algorithmic control:
 filter tree heap memopt load sort verbose
    0.1 TRUE TRUE  FALSE TRUE    2    TRUE

Absolute minimum support count: 9 

set item appearances ...[0 item(s)] done [0.00s].
set transactions ...[169 item(s), 9835 transaction(s)] done [0.00s].
sorting and recoding items ... [157 item(s)] done [0.00s].
creating transaction tree ... done [0.00s].
checking subsets of size 1 2 3 4 5 6 done [0.01s].
writing ... [410 rule(s)] done [0.00s].
creating S4 object  ... done [0.00s].
> rules <- head(rules, by="lift")
> rules
set of 6 rules 
> 
> ### save rules as PMML
> write.PMML(rules, file = "rules.xml")
Error in write.PMML(rules, file = "rules.xml") : 
  Package 'pmml' needs to be  installed!
Execution halted
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: 'arules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'arules', 'seriation', 'colorspace', 'vcd', 'igraph',
  'scatterplot3d', 'ggplot2', 'tibble', 'tidyr', 'dplyr', 'DT',
  'plotly', 'visNetwork'

Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'shiny', 'shinythemes', 'htmlwidgets'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'scatterplot3d', 'pixmap', 'plotrix', 'mvtnorm', 'deSolve',
  'combinat', 'multcompView', 'gWidgets2', 'gWidgets2tcltk'

Packages suggested but not available for checking: 'akima', 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'jsonlite', 'processx', 'tibble', 'uuid', 'V8'

Packages suggested but not available for checking:
  'cli', 'htmlwidgets', 'knitr', 'rmarkdown'

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.
'LazyData' is specified without a 'data' directory
Package required but not available: 'digest'

Packages suggested but not available for checking:
  'Hmisc', 'xtable', 'R2HTML', 'knitr'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'haven', 'readr', 'vroom', 'stringr', 'zoo', 'shiny',
  'miniUI', 'rstudioapi'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'truncnorm', 'mixsqp', 'SQUAREM', 'etrunct', 'invgamma'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'exact2x2', 'exactci', 'bpcp', 'coin', 'perm', 'ssanv'

Package suggested but not available for checking: 'bootstrap'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BatchExperiments', 'BatchJobs', 'BBmisc', 'checkmate', 'corrplot',
  'ggplot2', 'llama', 'mlr', 'parallelMap', 'ParamHelpers', 'plyr',
  'reshape2', 'RWeka', 'stringr', 'yaml'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qtl', 'gtools', 'fields', 'RColorBrewer'

Packages suggested but not available for checking:
  'knitr', 'formatR', 'digest'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/asmapvignette.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ape', 'raster', 'sna'
Running examples in 'asnipe-Ex.R' failed
The error most likely occurred in:

> ### Name: get_network
> ### Title: Calculating Weighted Network
> ### Aliases: get_network
> 
> ### ** Examples
> 
> 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
> 
> ## test if one predicts the other via a mantel test (must be loaded externally)
> library(ape)
Error in library(ape) : there is no package called 'ape'
Execution halted
Packages required but not available: 'splancs', 'Hmisc', 'shapefiles'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'sem', 'polycor'
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'gee', 'mvtnorm', 'fields', 'matrixStats'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dae', 'ggplot2', 'reshape', 'plyr', 'dplyr', 'stringr',
  'RColorBrewer', 'foreach', 'doParallel'

Packages suggested but not available for checking:
  'testthat', 'emmeans', 'lmerTest', 'pbkrtest', 'R.rsp'

Package which this enhances but not available for checking: 'asreml'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Packages unavailable to check Rd xrefs: 'assertive.properties', 'assertive.types'
'LazyData' is specified without a 'data' directory
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:
  'assertive.base', 'assertive.properties', 'assertive.types'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

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: 'assertive.base', 'assertive.types'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive.base', 'assertive.properties', 'assertive.types',
  'assertive.numbers', 'assertive.strings', 'assertive.datetimes',
  'assertive.files', 'assertive.sets', 'assertive.matrices',
  'assertive.models', 'assertive.data', 'assertive.data.uk',
  'assertive.data.us', 'assertive.reflection', 'assertive.code',
  'knitr'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive.base', 'assertive.types', 'stringi'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'testthat', 'data.table', 'dplyr', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'magrittr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
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:
  'VineCopula', 'mvtnorm', 'numDeriv', 'mvQuad', 'ggplot2', 'Rdpack'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'doParallel', 'e1071', 'foreach', 'ggplot2', 'randomForest',
  'reshape2', 'stringr', 'tree'

Packages suggested but not available for checking:
  'gtable', 'iterators', 'klaR', 'stringi', 'knitr', 'rmarkdown',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'sp', 'rgdal', 'maptools'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'mvtnorm', 'knitr', 'magrittr', 'dplyr'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rootSolve'
Packages required but not available:
  'shiny', 'rmarkdown', 'arules', 'arulesViz', 'shinyMatrix', 'plotly',
  'dplyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'aster'
Package unavailable to check Rd xrefs: 'aster'
Running 'asterdata.R'
  Comparing 'asterdata.Rout' to 'asterdata.Rout.save' ... OK
  Running 'constancy.R'
  Comparing 'constancy.Rout' to 'constancy.Rout.save' ... OK
  Running 'echinacea-cond.R'
Running the tests in 'tests/echinacea-cond.R' failed.
Complete output:
  > 
  >  #### copied from help page for function library
  > 
  >  pkg <- "aster"
  >  library(pkg, character.only = TRUE)
  Error in library(pkg, character.only = TRUE) : 
    there is no package called 'aster'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'formatR', 'webshot', 'BiocStyle', 'RUnit', 'BiocGenerics',
  'plotly', 'lazyeval', 'dplyr', 'ggmap', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'runTests.R'
Running the tests in 'tests/runTests.R' failed.
Complete output:
  > BiocGenerics:::testPackage("asteRisk")
  Error in loadNamespace(x) : there is no package called 'BiocGenerics'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: 'trust'

Package suggested but not available for checking: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'fields', 'foreach', 'IDPmisc', 'iterators',
  'multitaper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
beamDiskOverlap: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for 'spline'
galage: no visible global function definition for 'integrate'
lumdist: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
Packages required but not available: 'rwt', 'wavethresh'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'decon', 'kedd', 'locfit', 'ks', 'kerdiest', 'sm', 'ICV', 'OSCV'

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
Packages required but not available: 'sn', 'skewt', 'gamlss.dist'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'RColorBrewer'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'rmarkdown', 'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'doBy', 'plyr', 'reshape2', 'Hmisc', 'settings', 'DescTools',
  'effsize'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/atable_usage.rnw'
   'inst/doc/extending.Rnw'
   'inst/doc/modifying.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forecast', 'Rcpp', 'Rdpack', 'seasonal', 'stlplus', 'stR',
  'timeSeries', 'TSA', 'tseries', 'xts', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gstat', 'sp', 'rgeos', 'foreach', 'doSNOW', 'snow', 'FNN', 'Rcpp'

Packages suggested but not available for checking:
  'raster', 'rgdal', 'rtop'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
get.est.ATT: no visible global function definition for 'tail'
get.est.MT: no visible global function definition for 'tail'
get.est.simple: no visible global function definition for 'tail'
newton.r: no visible global function definition for 'tail'
plot.ATE: no visible global function definition for 'par'
plot.ATE: no visible global function definition for 'axis'
plot.ATE: no visible global function definition for 'abline'
plot.ATE: no visible global function definition for 'lines'
plot.ATE: no visible global function definition for 'legend'
plot.ATE: no visible global function definition for 'points'
print.summary.ATE: no visible global function definition for
  'printCoefmat'
summary.ATE: no visible global function definition for 'qnorm'
summary.ATE: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis legend lines par pnorm points printCoefmat qnorm tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages required but not available: 'httr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
atmcmc : rmvtnorm: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'runif'
atmcmc: no visible global function definition for 'par'
atmcmc: no visible global function definition for 'lm'
atmcmc: no visible global function definition for 'lines'
atmcmc: no visible global function definition for 'var'
atmcmc: no visible global function definition for 'cov'
atmcmc: no visible global function definition for 'quantile'
atmcmc: no visible global function definition for 'sd'
plotmcmc: no visible global function definition for 'pdf'
plotmcmc: no visible global function definition for 'par'
plotmcmc: no visible global function definition for 'dev.new'
plotmcmc: no visible global function definition for 'png'
plotmcmc: no visible global function definition for 'hist'
plotmcmc: no visible global function definition for 'dev.off'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf png quantile rnorm runif sd
  var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
Packages required but not available:
  'DiceDesign', 'lhs', 'metRology', 'msm', 'sensitivity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DoE.base', 'hierNet', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RSEIS'
PlotAtm.lin : scale_image: no visible global function definition for
  'heat.colors'
PlotAtm.lin : scale_image: no visible global function definition for
  'par'
PlotAtm.lin : scale_image: no visible global function definition for
  'sd'
PlotAtm.lin : scale_image: no visible global function definition for
  'approx'
PlotAtm.lin : scale_image: no visible global function definition for
  'image'
PlotAtm.lin : scale_image: no visible global function definition for
  'axis'
PlotAtm.lin : scale_image: no visible global function definition for
  'mtext'
PlotAtm.lin: no visible global function definition for 'arrows'
PlotAtm.lin: no visible global function definition for 'text'
PlotAtm.lin: no visible global function definition for 'polygon'
sky.colors: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Package required but not available: 'partykit'

Packages suggested but not available for checking: 'trtf', 'mlbench'

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

Packages suggested but not available for checking:
  'zoo', 'knitr', 'chron', 'timeDate', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'desc', 'glue', 'knitr', 'magrittr', 'rmarkdown', 'roxygen2',
  'stringr'

Package suggested but not available for checking: 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'curl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'spelling'
'LazyData' is specified without a 'data' directory
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:
  'data.table', 'magrittr', 'glue', 'pbs', 'dlnm', 'lubridate',
  'mvmeta', 'tsModel', 'lme4', 'arm', 'tibble', 'stringr', 'ggplot2',
  'progress'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'RUnit', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines
Consider adding
  importFrom("graphics", "lines")
to your NAMESPACE file.
Package required but not available: 'randomForest'

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:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggbeeswarm', 'ggthemes'

VignetteBuilder package required for checking but not installed: 'knitr'

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', 'gridExtra', 'hnp', 'scales'

Packages suggested but not available for checking:
  'jsonlite', 'knitr', 'r2d3', 'randomForest', 'rmarkdown', 'testthat',
  'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
simulateD: no visible global function definition for 'rgamma'
simulateT: no visible global function definition for 'runif'
simulateT: no visible global function definition for 'rbeta'
simulateT: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Packages required but not available:
  'emmeans', 'dplyr', 'flextable', 'ggplot2', 'moments', 'multcomp',
  'multcompView', 'Rdpack', 'stringi', 'officer', 'reshape2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pander', 'testthat', 'agricolae'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'Formula', 'nleqslv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'countrycode', 'dplyr', 'httr', 'magrittr', 'rlang',
  'stringi', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'data.table', 'knitr', 'readr', 'rmarkdown', 'sf',
  'testthat', 'unmarked'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'forecast', 'caret', 'ipred',
  'flexclust', 'e1071', 'randomForest'

Package which this enhances but not available for checking: 'rPython'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'stringdist', 'reshape2', 'lsa', 'flexclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rjags', 'ProbYX', 'coda', 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vegan', 'maps', 'mapdata', 'plyr', 'R.utils', 'simba', 'httr',
  'jsonlite', 'sp', 'maptools', 'ggplot2', 'gtools', 'jose',
  'betapart', 'curl'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'shiny', 'shinyjs', 'htmltools', 'yaml'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xgboost', 'e1071', 'abind', 'caret', 'entropy', 'lsr', 'CORElearn',
  'infotheo', 'minerva', 'party'

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', 'checkmate', 'broom', 'moments', 'diptest', 'mclust',
  'ggplot2', 'tibble', 'hexbin', 'progress'

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

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spam', 'fields', 'filehashSQLite', 'filehash', 'LatticeKrig', 'FNN',
  'filematrix', 'Rcpp', 'RSpectra', 'RcppEigen', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colorspace', 'fields', 'mapproj', 'ggplot2', 'maps', 'MBA'

Packages suggested but not available for checking:
  'abind', 'testthat', 'spatstat.geom', 'gear', 'broom', 'gridExtra',
  'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'formatR', 'knitr', 'magrittr', 'purrr', 'remotes', 'yaml'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'ggplot2', 'maptools', 'gpclib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rlang', 'dplyr', 'lme4', 'gbm', 'e1071', 'tibble', 'glmmLasso',
  'EBMAforecast', 'foreach', 'doParallel', 'doRNG', 'ggplot2', 'knitr',
  'tidyr', 'purrr'

Packages suggested but not available for checking: 'rmarkdown', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pamr', 'siggenes', 'annotate', 'fgsea', 'org.Hs.eg.db',
  'RColorBrewer', 'ConsensusClusterPlus', 'Rtsne', 'clusterProfiler',
  'msigdbr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'XML', 'plyr', 'plotrix', 'seqinr', 'ade4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'zoo', 'lgarch'

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

Packages suggested but not available for checking:
  'roxygen2', 'magrittr', 'webshot'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'maxLik', 'forecast', 'lubridate', 'tsutils',
  'ggplot2', 'gridExtra', 'strucchange', 'imputeTS', 'foreach',
  'doSNOW', 'zoo', 'lmtest', 'tseries', 'ggrepel', 'progress', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'purrr', 'httpuv', 'RJSONIO', 'stringdist', 'rstudioapi', 'rlang',
  'stringr', 'rlist', 'magrittr', 'memoise', 'glue', 'xml2',
  'base64enc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'ijtiff', 'magrittr', 'purrr', 'Rcpp', 'rlang', 'strex',
  'stringr'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'knitr', 'rmarkdown', 'spelling',
  'styler', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'prophet', 'dplyr', 'magrittr', 'lubridate', 'tidyr',
  'forecast', 'ggplot2', 'RcppRoll', 'shiny', 'shinycssloaders',
  'plotly'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'stringr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'clisymbols', 'crayon', 'tidytext', 'desc', 'glue',
  'jsonlite', 'memoise', 'SnowballC', 'stringdist', 'tibble', 'udapi',
  'yesno'

Packages suggested but not available for checking:
  'usethis', 'BiocInstaller', 'BiocManager', 'testthat'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'caret', 'knitr', 'rpart.plot', 'rmarkdown', 'e1071'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'purrr', 'ggplot2', 'janitor', 'knitr', 'rmarkdown',
  'lubridate', 'tidyr', 'ggrepel'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages suggested but not available for checking:
  'testthat', 'ps', 'ggplot2', 'gapminder'
'LazyData' is specified without a 'data' directory
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:
  'Evapotranspiration', 'ncdf4', 'raster', 'chron', 'maptools', 'sp',
  'zoo', 'xts'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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:
  'kohonen', 'shiny', 'htmlwidgets', 'bslib', 'rmarkdown', 'htmltools',
  'rclipboard', 'ggplot2', 'RColorBrewer', 'viridis', 'data.table',
  'DT', 'kernlab', 'fields', 'e1071', 'haven', 'readxl', 'readODS'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AWR', 'futile.logger', 'jsonlite', 'rJava'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'aws.signature', 'xml2', 'dplyr'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'aws.signature'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjson', 'aws.signature', 'httr', 'xml2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'xml2', 'jsonlite', 'aws.signature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'base64enc', 'aws.signature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'aws.signature', 'base64enc'

Packages suggested but not available for checking:
  'testthat', 'aws.s3', 'aws.iam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'aws.signature', 'tuneR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'httr', 'xml2', 'base64enc', 'digest', 'aws.signature'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'digest', 'base64enc'

Packages suggested but not available for checking:
  'testthat', 'aws.ec2metadata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'aws.signature'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'aws.signature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'httr', 'openssl', 'jsonlite', 'jose', 'R6', 'rappdirs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'httpuv', 'shiny', 'AzureRMR',
  'AzureGraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureAuth', 'AzureRMR', 'jsonlite', 'httr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureRMR', 'AzureGraph', 'openssl', 'httr', 'R6', 'processx'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'uuid', 'bcrypt', 'randomForest',
  'plumber', 'RestRserve', 'AzureKeyVault'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureRMR', 'curl', 'openssl', 'jsonlite', 'httr', 'uuid', 'vctrs'

Packages suggested but not available for checking:
  'AzureTableStor', 'mongolite', 'DBI', 'odbc', 'dplyr', 'testthat',
  'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureAuth', 'httr', 'jsonlite', 'openssl', 'curl', 'R6'

Packages suggested but not available for checking:
  'AzureRMR', 'vctrs', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'httr', 'jsonlite', 'openssl', 'jose', 'AzureRMR',
  'AzureGraph', 'AzureAuth'

Packages suggested but not available for checking:
  'AzureStor', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'httr', 'jsonlite', 'R6', 'openssl', 'AzureAuth',
  'AzureRMR', 'tibble', 'dplyr', 'tidyselect', 'DBI'

Packages suggested but not available for checking:
  'bit64', 'knitr', 'testthat', 'tidyr', 'AzureGraph', 'AzureStor',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'reticulate', 'plyr', 'DT', 'rstudioapi', 'htmltools',
  'servr', 'shiny', 'shinycssloaders'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', 'dplyr', 'jsonlite', 'foreach',
  'iterators'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureRMR', 'AzureStor', 'openssl', 'httr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureGraph', 'AzureAuth', 'httr', 'jsonlite', 'R6', 'uuid'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'httpuv', 'AzureStor'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'httr', 'mime', 'openssl', 'xml2', 'AzureRMR'

Packages suggested but not available for checking:
  'AzureAuth', 'readr', 'knitr', 'rmarkdown', 'jsonlite', 'testthat',
  'processx', 'uuid'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureRMR', 'AzureStor', 'jsonlite', 'openssl', 'httr', 'uuid',
  'vctrs'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'AzureAuth', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'AzureAuth', 'AzureVM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'AzureRMR', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'AzureKeyVault', 'AzureVMmetadata'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CRexp_set: no visible global function definition for 'runif'
b6e6rl: no visible global function definition for 'runif'
derand_RL: no visible global function definition for 'runif'
derandexp_RL: no visible global function definition for 'runif'
nahvyb_expt: no visible global function definition for 'runif'
roulete: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'
.generateTransform: no visible global function definition for 'sd'
.generateUnitHyperCube: no visible global function definition for
  'runif'
.makeBoundedSingleStep: no visible global function definition for
  'runif'
.makeBoundedStep: no visible global function definition for 'runif'
.makeStep: no visible global function definition for 'runif'
.staircaseSampling: no visible global function definition for 'runif'
GaussianPrior: no visible global function definition for 'qnorm'
LogNormalPrior: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Package required but not available: 'edgeR'

Packages suggested but not available for checking:
  'R.rsp', 'R.devices', 'R.utils'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'beautier', 'beastier', 'mauricer', 'tracerer', 'phangorn',
  'remotes', 'stringr', 'testit', 'xml2'

Packages suggested but not available for checking:
  'ape', 'curl', 'ggplot2', 'hunspell', 'knitr', 'lintr', 'nLTT',
  'rappdirs', 'rmarkdown', 'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'mice', 'norm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SPOT', 'checkmate', 'curl', 'data.table', 'dplyr', 'ggplot2',
  'golem', 'igraph', 'lubridate', 'markovchain', 'padr', 'rvest',
  'scales', 'simmer', 'slider', 'testthat', 'plyr', 'xml2'

Packages suggested but not available for checking:
  'batchtools', 'knitr', 'rpart.plot', 'simmer.plot', 'stringr',
  'tidyverse', 'usethis', 'vctrs'

VignetteBuilder package required for checking but not installed: 'knitr'

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.
Packages required but not available:
  'sybil', 'ReacTran', 'deSolve', 'ggplot2', 'reshape2', 'glpkAPI',
  'plyr', 'Rcpp', 'igraph', 'stringr', 'R.matlab', 'RcppArmadillo',
  'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rjags', 'ggplot2', 'reshape2'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'magrittr', 'pipeR', 'R6', 'testthat', 'shiny', 'knitr',
  'rstudioapi', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'magrittr', 'pipeR'
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:
  'clue', 'igraph', 'matrixcalc', 'reshape2', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'pander', 'fields', 'testthat', 'pcalg', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'mvtnorm', 'leaps'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'git2r'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dlstats', 'rvcheck', 'desc', 'usethis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'doParallel', 'mclust', 'kedd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'bayesplot', 'crayon', 'forestplot',
  'ggplot2', 'gridExtra', 'testthat', 'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'parsnip', 'hardhat', 'butcher', 'C50', 'withr', 'rsample', 'dplyr',
  'purrr', 'furrr', 'tibble', 'tidyr', 'rlang', 'earth', 'magrittr',
  'generics', 'dials'

Packages suggested but not available for checking:
  'testthat', 'AmesHousing', 'recipes', 'modeldata', 'covr',
  'yardstick'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'erah', 'HiClimR', 'XML', 'signal'

Packages suggested but not available for checking: 'R.rsp', 'mzR'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'mvtnorm'

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

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

Packages suggested but not available for checking:
  'ape', 'ggthemes', 'knitr', 'philr', 'propr', 'reshape2',
  'rmarkdown', 'robCompositions', 'testthat', 'vegan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'seqinr', 'Rpdb', 'scales', 'dplyr', 'Biostrings', 'readr',
  'progress'

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

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'scales', 'networkD3', 'testthat', 'fields', 'stringr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppDist', 'BH'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'qrng', 'mvtnorm', 'gtools', 'label.switching', 'coda',
  'future.apply', 'loo', 'RColorBrewer', 'bridgesampling', 'scales',
  'numDeriv', 'RcppArmadillo'

Packages suggested but not available for checking: 'future', 'gridExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjags', 'R2jags', 'ggplot2', 'ggExtra', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'colorspace', 'Formula', 'MBA', 'mvtnorm', 'sp'

Packages suggested but not available for checking:
  'akima', 'ff', 'ffbase', 'fields', 'gamlss', 'gamlss.dist', 'geoR',
  'rjags', 'BayesX', 'BayesXsrc', 'R2BayesX', 'mapdata', 'maps',
  'maptools', 'spatstat', 'spdep', 'zoo', 'keras', 'splines2',
  'sdPrior', 'statmod', 'glogis', 'glmnet', 'scoringRules', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

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

Package suggested but not available for checking: 'coda'

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rjags', 'runjags', 'coda', 'rstan'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'ggplot2', 'gridExtra', 'plyr', 'randomForest',
  'ranger', 'rfPermute', 'rlang', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'stringr', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'lme4', 'sva', 'affyPLM', 'FNN', 'fuzzyRankTests',
  'mnormt', 'affy', 'Biobase'

Package suggested but not available for checking: 'ArrayExpress'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gpairs'
'library' or 'require' calls to packages already attached by Depends:
  'grid' 'lattice'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'hist'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
Packages unavailable to check Rd xrefs: 'YaleToolkit', 'gpairs'
Packages required but not available:
  'qrcode', 'DT', 'miniUI', 'rstudioapi', 'shiny'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'shinytest', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 13825 marked UTF-8 strings
Packages required but not available:
  'magrittr', 'dplyr', 'data.table', 'downloader', 'sf', 'XML', 'httr',
  'rgdal', 'janitor', 'rio', 'jsonlite', 'stringr', 'memoise',
  'stringi', 'shiny', 'miniUI', 'rstudioapi', 'checkmate'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'vectools', 'misc3d', 'probhat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'mvnfast', 'Rdpack', 'RcppArmadillo', 'BH'

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

Packages suggested but not available for checking:
  'testthat', 'lme4', 'tmle'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rJava', 'bartMachineJARs', 'randomForest', 'missForest'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/the-BART-R-package.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'warbleR', 'pbapply', 'seewave', 'tuneR', 'fftw'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'knitr', 'kableExtra', 'viridis', 'png',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'knitr', 'prettydoc'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'png'
Package required but not available: 'openssl'

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

Packages suggested but not available for checking:
  'base64enc', 'checkmate', 'knitr', 'microbenchmark', 'openssl',
  'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'xml2', 'magrittr', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'rmarkdown', 'knitr', 'Lahman'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'testthat'

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

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

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

Packages suggested but not available for checking:
  'gWidgets2', 'gWidgets2tcltk', 'IDPmisc', 'pls'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'Biobase', 'covr', 'forcats', 'ggplot2', 'GO.db', 'GSEABase',
  'knitr', 'org.Hs.eg.db', 'reactome.db', 'rmarkdown', 'spelling',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sf', 'tibble', 'raster'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'R6', 'dplyr', 'htmltools', 'htmlwidgets'

Packages suggested but not available for checking:
  'jsonlite', 'lubridate', 'listviewer', 'openxlsx', 'shiny', 'knitr',
  'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'ggrepel', 'gridExtra', 'scales', 'directlabels', 'corrplot',
  'ggplotify', 'network', 'sna', 'dendextend', 'circlize',
  'PBSmapping', 'sp', 'operators', 'stringr', 'GGally',
  'statnet.common', 'ggnetwork', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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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
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Files named as vignettes but with no recognized vignette engine:
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(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages which this enhances but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'lubridate', 'scales', 'furrr', 'purrr', 'future', 'tibble', 'zoo',
  'crayon'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
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  'digest', 'fs', 'progress', 'R6', 'rappdirs', 'stringi', 'withr'

Packages suggested but not available for checking:
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  'future.batchtools', 'knitr', 'parallelMap', 'ranger', 'rmarkdown',
  'snow', 'testthat', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'hrbrthemes', 'httr', 'lubridate', 'magrittr', 'purrr', 'reshape2',
  'rvest', 'rworldmap', 'scales', 'stringi', 'stringr', 'tibble',
  'tidyr', 'xml2'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

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', 'reshape2', 'assertthat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'metRology', 'reshape', 'rstan', 'rstantools', 'mcmcse', 'scales',
  'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

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

> ### Name: anovaplot
> ### Title: anovaplot
> ### Aliases: anovaplot
> 
> ### ** Examples
> 
> set.seed(42)
> x1=rnorm(75,0,1)
> x2=rnorm(75,1,1)
> x3=rnorm(75,2,1)
> result=bayes.anova(n=1000,first=x1,second=x2,third=x3)
Error in loadNamespace(x) : there is no package called 'MCMCpack'
Calls: bayes.anova ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'coda', 'forecast'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'label.switching', 'foreach', 'doParallel', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'RISmed', 'testthat'
'LazyData' is specified without a 'data' directory
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: 'plyr', 'HDInterval'

Packages suggested but not available for checking:
  'testthat', 'foreach', 'doParallel'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'coda', 'tidyr', 'dplyr', 'stringr',
  'ggplot2', 'magrittr', 'fdrtool', 'Formula', 'loo', 'RcppParallel',
  'BH', 'RcppEigen', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'
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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:
  'Rcpp', 'abind', 'coda', 'mvtnorm', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppDist', 'mvtnorm'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rootSolve', 'truncdist', 'mvtnorm', 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'eha', 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'ggplot2', 'loo', 'dplyr', 'reshape2',
  'rlang', 'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'pbapply', 'mvtnorm', 'stringr', 'gtools', 'MatrixModels',
  'Rcpp', 'hypergeo', 'RcppEigen'

Packages suggested but not available for checking:
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  'xtable', 'languageR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayesplot', 'gridExtra', 'ggplot2', 'forecast', 'loo', 'Rcpp',
  'rstan', 'rstantools', 'RcppParallel', 'bridgesampling',
  'StanHeaders', 'astsa', 'lubridate', 'prophet', 'zoo', 'BH',
  'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayesplot', 'corrplot', 'ggplot2', 'gridExtra', 'loo', 'mlbench',
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'SemiPar', 'geometry',
  'BH', 'RcppEigen', '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: 'mvtnorm', 'coda'

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

Package suggested but not available for checking: 'ssym'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'coda', 'rjags'

Packages suggested but not available for checking: 'R2OpenBUGS', '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', 'Rcpp', 'knitr', 'readxl', 'xlsx', 'ggplot2', 'car',
  'crayon', 'bridgesampling', 'rhandsontable', 'shiny', 'pracma',
  'shinydashboard', 'shinythemes'

Packages suggested but not available for checking:
  'openxlsx', 'hexbin', 'magrittr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

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:
  'bnlearn', 'heatmaply', 'networkD3', 'plotly', 'rintrojs', 'shiny',
  'shinyAce', 'shinydashboard', 'shinytest', 'shinyWidgets', 'testthat'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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:
  'brms', 'parsnip', 'dplyr', 'purrr', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'rmarkdown', 'roxygen2', 'spelling',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'reshape2', 'ggplot2', 'tidyr', 'magrittr', 'tibble',
  'ggforce'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'patchwork'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'emulator', 'mvtnorm', 'tmvtnorm', 'IDPmisc', 'Rcpp',
  'ellipse', 'numDeriv', 'msm', 'DHARMa', 'gap', 'bridgesampling'

Packages suggested but not available for checking:
  'DEoptim', 'lhs', 'sensitivity', 'knitr', 'rmarkdown', 'roxygen2',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'mcmcse', 'coda', 'PottsUtils', 'rstan', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'coda', 'fields', 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayesTFR', 'wpp2019', 'hett', 'car', 'coda', 'data.table'

Packages suggested but not available for checking:
  'wpp2017', 'wpp2015', 'wpp2012', 'wpp2010'

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

Packages suggested but not available for checking:
  'BBcor', 'BGGM', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'optimx', 'ghyp', 'fAsianOptions', 'coda', 'Rcpp', 'lme4',
  'data.table', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'Rdpack', 'igraph', 'dplyr', 'sets', 'relations',
  'tidyr', 'purrr', 'rlang', 'PerMallows', 'HDInterval', 'PLMIX',
  'cowplot', 'RcppArmadillo'

Packages suggested but not available for checking:
  'R.rsp', 'testthat', 'label.switching', 'readr', 'stringr', 'gtools',
  'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'pracma', 'tmvtnorm', 'LaplacesDemon', 'HDInterval', 'coda'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'spelling', 'tgp', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'compute.es', 'knitr', 'rmarkdown', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MCMCpack', 'FastGP', 'Rcpp', 'coda', 'mvtnorm', 'RcppArmadillo'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'lubridate', 'MCMCpack', 'progress',
  'purrr', 'Rcpp', 'rlang', 'tictoc', 'tidyr', 'magrittr', 'future',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'testthat', 'spelling', 'knitr', 'rmarkdown', 'ggforce',
  'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'igraph', 'mvnfast', 'Rcpp', 'spam', 'RcppArmadillo'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'RColorBrewer', 'fields', 'doBy', 'qtl', 'graph',
  'bnlearn', 'qtlnet'

Packages suggested but not available for checking:
  'Rgraphviz', 'shiny', 'googleVis', 'cyjShiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
noninform_prior : a : f1: no visible global function definition for
  'pbeta'
noninform_prior : a : f1: no visible global function definition for
  'dbeta'
noninform_prior : a: no visible global function definition for
  'integrate'
noninform_prior: no visible global function definition for 'rbeta'
noninform_prior: no visible global function definition for 'optim'
postNullFun : b : f1: no visible global function definition for 'pbeta'
postNullFun : b : f1: no visible global function definition for 'dbeta'
postNullFun : b: no visible global function definition for 'integrate'
prior_prob : a : f1: no visible global function definition for 'pbeta'
prior_prob : a : f1: no visible global function definition for 'dbeta'
prior_prob : a: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
Packages required but not available: 'nimble', 'FNN', 'StatMatch'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggridges', 'glue', 'reshape2', 'rlang',
  'tibble', 'tidyselect'

Packages suggested but not available for checking:
  'ggfortify', 'gridExtra', 'hexbin', 'knitr', 'loo', 'RColorBrewer',
  'rmarkdown', 'rstan', 'rstanarm', 'rstantools', 'scales',
  'shinystan', 'testthat', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayesTFR', 'bayesLife', 'MortCast', 'abind', 'data.table',
  'wpp2019', 'wpp2012', 'rworldmap', 'fields', 'googleVis', 'reshape2',
  'plyr'

Packages suggested but not available for checking:
  'wpp2017', 'wpp2015', 'wpp2010'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'carData', 'caTools', 'coda', 'dplyr', 'ggplot2', 'ggridges',
  'reshape2', 'rlang', 'texreg', 'tidyr', 'HDInterval', 'ROCR'

Packages suggested but not available for checking:
  'brms', 'knitr', 'MCMCpack', 'rjags', 'R2jags', 'R2WinBUGS',
  'rmarkdown', 'rstan', 'rstanarm', 'runjags', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'LaplacesDemon', 'lavaan', 'coda', 'Rdpack', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

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

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

Packages suggested but not available for checking: 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'snowfall', 'abind', 'splines2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'TeachingSampling'

VignetteBuilder package required for checking but not installed: 'knitr'
Namespaces in Imports field not imported from:
  'MASS' 'Matrix' 'stats'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'TeachingSampling'
Packages required but not available:
  'Rcpp', 'dplyr', 'ggplot2', 'rstan', 'lme4'

Package suggested but not available for checking: 'gridExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MCMCpack', 'FastGP', 'Rcpp', 'coda', 'dplyr', 'reshape2', 'ggplot2',
  'ape', 'RcppArmadillo'

Packages suggested but not available for checking:
  'spduration', 'countrycode'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'xml2', 'igraph', 'tikzDevice', 'RcppArmadillo'

Packages suggested but not available for checking:
  'R.rsp', 'BDgraph', 'data.table', 'plyr', 'scrime'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking:
  'simsurv', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'BayesFactor', 'bayesQR', 'blavaan', 'bridgesampling', 'brms',
  'dplyr', 'effectsize', 'emmeans', 'GGally', 'ggplot2', 'ggridges',
  'httr', 'knitr', 'lavaan', 'lme4', 'logspline', 'mclust',
  'mediation', 'modelbased', 'parameters', 'performance', 'rmarkdown',
  'rstan', 'rstanarm', 'see', 'spelling', 'stringr', 'testthat',
  'tidyr', 'tweedie'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'coda', 'wpp2019', 'data.table'

Packages suggested but not available for checking:
  'rworldmap', 'snowFT', 'googleVis', 'rgdal', 'sp', 'wpp2017',
  'wpp2015', 'wpp2012', 'wpp2010', 'ggplot2'

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

Package suggested but not available for checking: 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tgp', 'BayesTree', 'bartMachine'
Packages required but not available: 'coda', 'matrixStats', 'rjags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking:
  'knitr', 'faraway', 'hdi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'StanHeaders', 'coda', 'bnlearn', 'ggplot2', 'bayesplot',
  'viridis', 'reshape2', 'dplyr'

Package suggested but not available for checking: 'loo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shapefiles', 'sp', 'maptools', 'colorspace', 'coda'

Packages suggested but not available for checking:
  'spdep', 'akima', 'gpclib', 'rgeos'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'R2BayesX'
GNU make is a SystemRequirements.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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 suggested but not available for checking: 'coda'
'library' or 'require' call to 'coda' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in 'BayHaz-Ex.R' failed
The error most likely occurred in:

> ### Name: BayHaz-package
> ### Title: R Functions for Bayesian Hazard Rate Estimation
> ### Aliases: BayHaz-package BayHaz
> ### Keywords: package survival smooth
> 
> ### ** Examples
> 
> # the following analysis uses CPP hazard rates but can be easily adapted to BPS hazard rates
> 
> # set RNG seed (for example reproducibility only)
> set.seed(1234)
> 
> # select a CPP prior distribution (with default number of CPP jumps)
> hypars<-CPPpriorElicit(r0 = 0.1, H = 1, T00 = 50, M00 = 2, extra = 0)
> 
> # plot some sample prior hazard rates
> CPPplotHR(CPPpriorSample(ss = 10, hyp = hypars), tu = "Year")
> 
> # load a data set
> data(earthquakes)
> 
> # generate a posterior sample
> post<-CPPpostSample(hypars, times = earthquakes$ti, obs = earthquakes$ob)
> 
> # check that no additional CPP jumps are needed:
> # if this probability is not negligible,
> # go back to prior selection stage and increase 'extra'
> ecdf(post$sgm[,post$hyp$F])(post$hyp$T00+3*post$hyp$sd)
[1] 0
> 
> # plot some posterior hazard rate summaries
> CPPplotHR(post , tu = "Year")
> 
> # save the posterior sample to file for later use
> save(post, file = "post.rda")
> 
> # convert the posterior sample into an MCMC object
> post<-CPPpost2mcmc(post)
Loading required package: coda
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'coda'
Warning in CPPpost2mcmc(post) :
  Package 'coda' is not available: a 'matrix' is returned...
> 
> # take advantage of package 'coda' for output diagnostics
> pdf("diagnostics.pdf")
> traceplot(post)
Error in traceplot(post) : could not find function "traceplot"
Execution halted
Packages required but not available:
  'coda', 'hexbin', 'rjags', 'runjags', 'Luminescence', 'ArchaeoPhases'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfortify', 'lme4', 'magrittr', 'matrixStats',
  'reshape2', 'rstiefel', 'rlang', 'scales', 'tibble', 'tidyr',
  'tidyverse'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dataRetrieval', 'digest', 'lubridate', 'memoise', 'plyr'

Packages suggested but not available for checking:
  'devtools', 'dplyr', 'fitdistrplus', 'imputeTS', 'knitr', 'markdown',
  'pander', 'readxl', 'rmarkdown', 'sessioninfo', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pbapply', 'psych', 'wdm', 'bayeslincom'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
LaplaceMetropolis_admkr: no visible binding for global variable
  'median'
LaplaceMetropolis_admkr: no visible global function definition for
  'mad'
LaplaceMetropolis_gaussian: no visible binding for global variable
  'median'
LaplaceMetropolis_gaussian: no visible global function definition for
  'mad'
cost_admkr: no visible global function definition for 'sd'
cov_chol: no visible global function definition for 'qchisq'
cov_chol_admkr: no visible global function definition for 'qchisq'
gibbs_admkr_erro: no visible global function definition for 'rnorm'
gibbs_admkr_erro: no visible global function definition for 'runif'
gibbs_admkr_nw: no visible global function definition for 'qnorm'
gibbs_admkr_nw: no visible global function definition for 'rnorm'
gibbs_admkr_nw: no visible global function definition for 'runif'
loglikelihood_admkr: no visible global function definition for 'sd'
margin_like_admkr: no visible global function definition for 'sd'
np_gibbs: no visible global function definition for 'qnorm'
np_gibbs: no visible global function definition for 'rnorm'
np_gibbs: no visible global function definition for 'runif'
np_gibbs: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
Packages required but not available:
  'DEoptim', 'aws', 'ggplot2', 'reshape2', 'shiny'

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

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

Packages suggested but not available for checking:
  'glmnet', 'BiocManager', 'Biostrings'

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

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

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

Packages suggested but not available for checking:
  'emdbook', 'rms', 'ggplot2', 'RUnit', 'MuMIn', 'AICcmodavg', 'Hmisc',
  'optimx', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mle2.Rnw'
   'inst/doc/quasi.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bbmm.contour: no visible global function definition for 'na.omit'
bbmm.contour: no visible global function definition for 'optimize'
bbmm.contour: no visible global function definition for 'contour'
bbmm.contour: no visible global function definition for 'points'
bbmm.contour: no visible global function definition for 'lines'
brownian.bridge: no visible global function definition for 'sd'
brownian.motion.variance: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
Package required but not available: 'ape'

Packages suggested but not available for checking: 'coda', 'geiger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
Undefined global functions or variables:
  runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages required but not available:
  'checkmate', 'data.table', 'lgr', 'mlr3misc', 'paradox', 'R6'

Packages suggested but not available for checking:
  'adagio', 'GenSA', 'knitr', 'nloptr', 'progressr', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'setRNG', 'Hmisc', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'HI', 'locfit', 'lme4', 'secr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pbapply', 'Formula', 'expint', 'statmod'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'progress', 'jagsUI', 'ggrepel', 'geofacet', 'ggplot2', 'stringr',
  'rgdal', 'dplyr', 'sf', 'latticeExtra', 'rappdirs', 'sbtools'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'c3net', 'infotheo', 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'glmnet', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'RcmdrMisc', 'Rcmdr', 'car', 'flexclust', 'clv'

Package suggested but not available for checking: 'rgl'

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

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'DBI', 'crul', 'dbplyr', 'dplyr', 'tibble', 'glue',
  'jsonlite', 'leaflet', 'leaflet.extras', 'purrr', 'readr', 'readxl',
  'rlang', 'sf', 'tidyselect', 'xml2'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'rmarkdown', 'testthat', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'biclust', 'isa2'

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

Packages suggested but not available for checking:
  'R2jags', 'R2OpenBUGS', 'ggplot2', 'INLA', 'splancs', 'ldr', 'shiny',
  'shinythemes', 'knitr', 'rmarkdown', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BMA', 'leaps', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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: 'gee'
Package unavailable to check Rd xrefs: 'gee'
Packages required but not available:
  'rjags', 'coda', 'knitr', 'crayon', 'plyr'

Package suggested but not available for checking: 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'mclust', 'ggplot2', 'ggridges', 'magrittr', 'purrr',
  'ggforce', 'dplyr', 'scales', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'mcclust', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'bcdata', 'httr', 'rappdirs', 'progress', 'xml2', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'future.apply', 'future', 'ggplot2', 'glue',
  'raster', 'rgdal', 'rgeos', 'sp', 'lwgeom', 'testthat', 'withr',
  'stars'

VignetteBuilder package required for checking but not installed: 'knitr'

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
Packages required but not available: 'Rcpp', 'plyr'

Packages suggested but not available for checking: 'knitr', 'circular'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/bcpa.rnw'
(Is a VignetteBuilder field missing?)

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

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

Packages suggested but not available for checking:
  'DNAcopy', 'coda', 'strucchange', 'vegan', 'ggplot2', 'igraph'

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

Packages suggested but not available for checking:
  'BRugs', 'R2WinBUGS', 'rjags'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mcclust', 'nFactors', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'data.table', 'batchelor', 'kBET', 'splatter', 'scater', 'knitr',
  'lisi', 'harmony', 'dlfUtils', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/simExperiment.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bdDwC', 'DT', 'data.table', 'finch', 'knitr', 'rgbif', 'shiny',
  'shinyBS', 'shinydashboard', 'shinyjs', 'spocc', 'yaml'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rmarkdown', 'knitr', 'shiny', 'shinydashboard', 'shinyjs',
  'leaflet', 'DT', 'data.table', 'rgbif', 'spocc', 'finch', 'bdDwC',
  'bdchecks'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyBS', 'shinydashboard', 'shinyjs', 'shinyFiles'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* DONE
Status: 1 ERROR
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenOrd', 'MultiOrd', 'stringdist', 'rgl', 'RSQLite', 'DBI'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'tibble', 'jsonlite', 'httr', 'dplyr', 'tidyr',
  'ggplot2', 'ggpubr', 'randomcoloR', 'purrr', 'sf', 'tmaptools',
  'tmap'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tinytest'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'digest', 'R6', 'rlist'

Packages suggested but not available for checking:
  'cld2', 'knitr', 'rex', 'rjson', 'rmarkdown', 'rtweet', 'stringi',
  'stringr', 'testthat', 'tuber'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'maps', 'plotrix', 'sqldf', 'plyr', 'taxize', 'treemap', 'ggplot2',
  'chron', 'leafletR', 'rgdal'

Package suggested but not available for checking: 'rinat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'foreach', 'doParallel', 'DWreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plm', 'Formula', 'Hmisc', 'deSolve', 'pracma', 'caTools',
  'matrixStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'DT', 'haven', 'xtable', 'rtf', 'plyr', 'sas7bdat',
  'WriteXLS', 'rJava', 'devtools'

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

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', 'fpc', 'ggplot2', 'magrittr', 'mclust', 'purrr',
  'raster', 'tibble', 'tidyr', 'yaml', 'rlang'

Packages suggested but not available for checking:
  'spelling', 'gridExtra', 'hexbin', 'igraph', 'knitr', 'rmarkdown',
  'stringr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'base64enc', 'httpuv', 'jsonlite', 'magrittr', 'mime',
  'stringr', 'webutils'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fdrtool', 'igraph', 'knitr', 'Rcpp', 'assertthat', 'RcppArmadillo',
  'BH'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'vioplot'
Package unavailable to check Rd xrefs: 'vioplot'
Errors in running code in vignettes:
when running code in 'beanplot.Rnw'
  ...
+     names = 1:3)

> beanplot(bimodal, uniform, normal, ylim = ylim, main = "beanplot", 
+     col = c("#CAB2D6", "#33A02C", "#B2DF8A"), border = "#CAB2D6")

> library("vioplot")

  When sourcing 'beanplot.R':
Error: there is no package called 'vioplot'
Execution halted

  'beanplot.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'beanplot.Rnw' using Sweave

Error: processing vignette 'beanplot.Rnw' failed with diagnostics:
 chunk 4 (label = singers) 
Error in library("vioplot") : there is no package called 'vioplot'

--- failed re-building 'beanplot.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'loo', 'StanHeaders', 'BH',
  'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'shiny', 'rmarkdown', 'pander', 'shinythemes', 'DT',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'httr', 'DT', 'shiny', 'jsonlite', 'googleVis',
  'shinydashboard', 'ggplot2', 'stringr', 'chron', 'gtable', 'scales',
  'htmltools', 'httpuv', 'xtable', 'stringi', 'magrittr',
  'htmlwidgets', 'Rcpp', 'munsell', 'colorspace', 'plyr', 'yaml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'assertive', 'beautier', 'phangorn', 'pryr', 'rappdirs',
  'remotes', 'rJava', 'stringr', 'xml2'

Packages suggested but not available for checking:
  'hunspell', 'knitr', 'rmarkdown', 'spelling', 'testit', 'testthat',
  'tracerer'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'assertive', 'pryr', 'rappdirs', 'seqinr', 'stringr', 'testit'

Packages suggested but not available for checking:
  'spelling', 'devtools', 'knitr', 'ggplot2', 'hunspell', 'lintr',
  'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'data.table', 'LinkedMatrix', 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'neo2R', 'visNetwork', 'dplyr', 'readr', 'stringr', 'shiny', 'DT',
  'htmltools', 'miniUI', 'rstudioapi'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'biomaRt', 'GEOquery', 'base64enc', 'webshot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'testthat', 'VennDiagram', 'data.table', 'R.utils', 'yaml'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nlmrt', 'nlstools', 'nls2', 'ggplot2', 'reshape2'

Packages suggested but not available for checking:
  'openxlsx', 'knitr', 'dplyr', 'tidyr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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: 'cranlogs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BiasedUrn', 'data.tree', 'DiagrammeR', 'DiagrammeRsvg', 'ggplot2',
  'googlesheets4', 'gridExtra', 'gtable', 'knitr', 'rmdpartials',
  'ufs', 'viridis', 'yum'

Packages suggested but not available for checking:
  'htmltools', 'kableExtra', 'openxlsx', 'png', 'rmarkdown',
  'rstudioapi', 'rsvg', 'webshot'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr'

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

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

Packages suggested but not available for checking:
  'testthat', 'sf', 'sp', 'stars', 'covr', 'knitr', 'rmarkdown',
  'ggplot2', 'rasterVis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'extraDistr', 'Formula', 'magic', 'numbers', 'Rcpp', 'Rdpack',
  'rstan', 'rstantools', 'BH', 'RcppEigen', '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:
  'lpSolveAPI', 'ucminf', 'quadprog', 'Rcpp'

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:
  'benchmarkme', 'covr', 'DT', 'testthat'

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

Packages suggested but not available for checking:
  'covr', 'DT', 'ggplot2', 'knitr', 'RcppZiggurat', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'covr', 'dplyr', 'forcats', 'ggbeeswarm', 'ggplot2', 'ggridges',
  'mockery', 'scales', 'testthat', 'tidyr', 'vctrs', 'withr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'jsonlite', 'httr'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'DEoptim'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/BENMMI_User_Manual.Rnw'
   'inst/doc/FAQ.Rnw'
(Is a VignetteBuilder field missing?)

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ergm', 'network', 'coda', 'MCMCpack', 'mvtnorm', 'matrixcalc',
  'statnet.common'

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

Packages suggested but not available for checking:
  'RColorBrewer', 'pbapply', 'knitr', 'rmarkdown', 'gstat', 'RCurl',
  'colorspace', 'vioplot', 'spatstat.geom', 'TeachingDemos', 'ade4'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'gsl', 'sfsmisc'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaps', 'glmnet', 'grpreg', 'pls'

Package which this enhances but not available for checking: 'caret'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'LambertW', 'nortest', 'dplyr', 'doParallel', 'foreach', 'doRNG',
  'recipes', 'tibble', 'butcher', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'scales', 'rlang'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinydashboard', 'shinyWidgets', 'shinyBS',
  'shinyjs', 'tidyr', 'dplyr', 'readxl', 'ggplot2', 'rlist', 'DT',
  'stringr'

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

Packages suggested but not available for checking:
  'XML', 'sp', 'raster', 'DALEX', 'ggplot2'

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

Packages suggested but not available for checking:
  'gamlss.dist', 'knitr', 'rmarkdown', 'betareg'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
betafam: no visible global function definition for 'pnorm'
betafam: no visible global function definition for 'pchisq'
betafam: no visible global function definition for 'lm'
betafam: no visible global function definition for 'coefficients'
betafam: no visible global function definition for 'glm.fit'
betafam: no visible global function definition for 'gaussian'
betafam: no visible global function definition for 'glmnet'
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'stringr', 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'fastmatch', 'geometry', 'picante', 'rcdd', 'doSNOW',
  'foreach', 'snow', 'itertools'

Package suggested but not available for checking: 'vegan'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'flexmix', 'Formula', 'lmtest', 'modeltools', 'sandwich'

Packages suggested but not available for checking:
  'car', 'partykit', 'strucchange'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Package required but not available: 'Rcpp'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'grnn', 'ggplot2', 'plotly', 'urca', 'forecast', 'zoo', 'rmarkdown',
  'seasonal', 'stringr', 'dygraphs', 'shiny', 'miniUI', 'rstudioapi',
  'DT', 'webshot', 'RMySQL', 'digest', 'DBI', 'rjson', 'rvest', 'xml2',
  'lubridate', 'htmltools', 'httr', 'dplyr', 'sqldf'

Packages suggested but not available for checking:
  'mFilter', 'devtools', 'xts', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'progress', 'spelling', 'testthat'

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Guide.Rnw'
(Is a VignetteBuilder field missing?)

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.
Packages required but not available:
  'ltsa', 'Rcpp', 'MTS', 'forecast', 'RcppArmadillo', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'strucchange', 'zoo', 'forecast', 'sp', 'raster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bain', 'mvtnorm', 'pracma', 'lme4', 'extraDistr'

Packages suggested but not available for checking:
  'testthat', 'polycor', 'pscl', 'metafor', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'doBy', 'SoDA', 'Hmisc', 'mfp'

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
Packages required but not available:
  'sp', 'DescTools', 'spdep', 'maptools', 'rgdal', 'rlang', 'rgeos'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'rvest', 'tibble', 'magrittr', 'purrr', 'janitor',
  'progress', 'pxR', 'pins', 'dplyr', 'tidyRSS'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'covr', 'circlize', 'data.table', 'dplyr', 'ggplot2', 'knitr',
  'lavaan', 'magrittr', 'officer', 'plyr', 'png', 'psych', 'rmarkdown',
  'rvg', 'scales', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BEDMatrix', 'LinkedMatrix', 'symDMatrix', 'crochet', 'bigmemory',
  'synchronicity', 'ff', 'bit'

Packages suggested but not available for checking:
  'data.table', 'lme4', 'SKAT', 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'R6', 'assertthat', 'pryr', 'rvest', 'stringr', 'xml2'

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: 'BGLR', 'coda'
Package unavailable to check Rd xrefs: 'BGLR'
'LazyData' is specified without a 'data' directory
Running examples in 'BGGE-Ex.R' failed
The error most likely occurred in:

> ### Name: BGGE
> ### Title: Genotype x Environment models using regression kernel
> ### Aliases: BGGE
> 
> ### ** Examples
> 
> # multi-environment main genotypic model
> library(BGLR)
Error in library(BGLR) : there is no package called 'BGLR'
Execution halted
Packages required but not available:
  'BFpack', 'GGally', 'ggplot2', 'ggridges', 'mvnfast', 'network',
  'reshape', 'Rcpp', 'Rdpack', 'sna', 'RcppArmadillo', 'RcppDist',
  'RcppProgress'

Packages suggested but not available for checking:
  'abind', 'assortnet', 'networktools', 'mice', 'psych', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'devtools', 'testthat', 'covr', 'knitr', 'rmarkdown', 'dplyr',
  'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mvtnorm', 'car', 'combinat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'purrr', 'tibble', 'ggplot2', 'ggthemes',
  'gridExtra', 'readr', 'rlang', 'stringr', 'tidyr', 'progress',
  'Brobdingnag'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
block.gibbs: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
Packages required but not available:
  'mvtnorm', 'matrixcalc', 'miscTools', 'coda', 'EDISON', 'statmod',
  'sparseMVN', 'inline', 'LaplacesDemon', 'glmnet', 'CholWishart',
  'mnormt', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MCMCpack', 'quantreg', 'SparseM', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'bayesm', 'coda', 'GIGrvg', 'knitr', 'Rcpp', 'stochvol',
  'xts', 'zoo', 'RcppArmadillo', 'RcppProgress'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for 'par'
global: no visible global function definition for 'runif'
global: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'par'
mymcmc: no visible global function definition for 'rnorm'
mymcmc: no visible global function definition for 'runif'
mymcmc: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'lines'
plkhci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: 'FrF2'
Packages unavailable to check Rd xrefs: 'conf.design', 'FrF2'
Packages required but not available: 'doParallel', 'foreach', 'R2jags'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/BHMSMAfMRIvignette.Rnw'
(Is a VignetteBuilder field missing?)

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

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

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R2HTML', 'xtable'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/BHTSpackManual.Rnw'
(Is a VignetteBuilder field missing?)

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'DT', 'magrittr', 'rBiasCorrection', 'shiny',
  'shinydashboard', 'shinyjs'

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', 'stringr', 'humaniformat', 'httr'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'viridis', 'dendextend', 'randomcoloR', '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:
  'bibliometrixData', 'dimensionsR', 'dplyr', 'DT', 'factoextra',
  'FactoMineR', 'ggraph', 'ggplot2', 'ggrepel', 'igraph', 'networkD3',
  'pubmedR', 'RColorBrewer', 'rio', 'rscopus', 'shiny', 'SnowballC',
  'stringdist', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'plotly', 'shinycssloaders',
  'shinythemes', 'visNetwork', 'wordcloud2'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'tidyr', 'biclust', 'clusteval', 'doParallel', 'dplyr',
  'foreach', 'magrittr', 'nycflights13', 'phyclust'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'isa2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'Rcpp', 'pcalg', 'graph', 'Rgraphviz'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RPostgreSQL', 'rgeos', 'rgdal', 'sp', 'DBI', 'ape', 'sf',
  'fasterize', 'raster', 'doParallel', 'foreach'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'maptools', 'maps'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'Formula', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'alpaca', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'lavaan', 'lavaan.survey', 'mitools', 'survey', 'TAM'

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: 'igraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigmemory', 'foreach', 'biglm', 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
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: 'processx'

Packages suggested but not available for checking:
  'ff', 'ffbase', 'RSQLite', 'rjson', 'magrittr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'httr', 'haplo.stats'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'bigstatsr', 'proxy', 'furrr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Missing link or links in documentation object 'bigGP.exit.Rd':
  'mpi.exit' 'mpi.quit'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Packages required but not available:
  'bigmemory', 'ncvreg', 'Rcpp', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'testthat', 'R.rsp', 'glmnet', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'RSQLite', 'RODBC'

Package which this enhances but not available for checking: 'leaps'

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

Packages suggested but not available for checking: 'RSQLite', 'RODBC'

Package which this enhances but not available for checking: 'leaps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'minpack.lm', 'numDeriv', 'progress', 'rgl', 'robustbase',
  'scales', 'nleqslv'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'shiny', 'DT'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'bigmemory', 'RColorBrewer', 'colorspace', 'RcppArmadillo',
  'BH'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rcbalance', 'liqueueR', 'plyr', 'mvnfast'

Package suggested but not available for checking: 'optmatch'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'bigmemory.sri', 'BH'

Package suggested but not available for checking: 'testthat'

Packages which this enhances but not available for checking:
  'biganalytics', 'bigtabulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'bigmemory', 'synchronicity'
Checking should be performed on sources prepared by 'R CMD build'.
Packages unavailable to check Rd xrefs: 'bigmemory', 'synchronicity'
Packages required but not available:
  'foreach', 'bigassertr', 'doParallel', 'flock', 'parallelly',
  'RhpcBLASctl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'googleAuthR', 'googleCloudStorageR', 'jsonlite', 'httr',
  'assertthat'

Packages suggested but not available for checking:
  'shiny', 'knitr', 'rmarkdown', 'testthat', 'data.table', 'purrr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigassertr', 'data.table', 'parallelly', 'Rcpp'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'covr', 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LinkingTo' for
  'Rcpp' 'RcppArmadillo'
are unused as they have no 'include' directory
Packages required but not available:
  'assertthat', 'bit64', 'curl', 'DBI', 'gargle', 'glue', 'httr',
  'jsonlite', 'prettyunits', 'progress', 'Rcpp', 'rlang', 'tibble',
  'rapidjsonr'

Packages suggested but not available for checking:
  'covr', 'DBItest', 'dbplyr', 'dplyr', 'blob', 'hms', 'wk', 'readr',
  'sodium', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigstatsr', 'bigassertr', 'bigparallelr', 'bigsparser', 'bigreadr',
  'bigutilsr', 'data.table', 'foreach', 'ggplot2', 'magrittr', 'Rcpp',
  'vctrs', 'RcppArmadillo', 'rmio'

Packages suggested but not available for checking:
  'bindata', 'covr', 'dbplyr', 'dplyr', 'gaston', 'glue', 'Hmisc',
  'pcadapt', 'rmutil', 'RSpectra', 'RSQLite', 'R.utils', 'spelling',
  'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'bigassertr', 'RcppEigen', 'rmio'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigassertr', 'bigparallelr', 'cowplot', 'foreach', 'ggplot2', 'ps',
  'Rcpp', 'RSpectra', 'tibble', 'RcppArmadillo', 'rmio'

Packages suggested but not available for checking:
  'biglasso', 'bigmemory', 'bigreadr', 'covr', 'data.table', 'dplyr',
  'glmnet', 'hexbin', 'memuse', 'ModelMetrics', 'ppcor', 'RhpcBLASctl',
  'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigmemory', 'magrittr', 'matrixStats', 'R.utils', 'RcppEigen',
  'speedglm'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'Rcpp', 'bigmemory', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigmemory', 'biganalytics', 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'Rcpp', 'corrplot', 'RcppArmadillo', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'tree', 'randomForest', 'gbm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigassertr', 'bigparallelr', 'nabor', 'Rcpp', 'robustbase',
  'RSpectra'

Packages suggested but not available for checking:
  'covr', 'Gmedian', 'mvtnorm', 'rrcov', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'Rcpp', 'RcppArmadillo', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'data.table'
Packages required but not available:
  'gtools', 'ade4', 'pracma', 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'htmltools', 'magrittr', 'jsonlite', 'ggplot2',
  'scales', 'shiny', 'rlang'

Packages suggested but not available for checking:
  'RColorBrewer', 'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

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.
Malformed Description field: should contain one or more complete sentences.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for 'chisq.test'
rmultnom: no visible global function definition for 'runif'
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
Packages required but not available: 'xts', 'zoo'

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

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

Package suggested but not available for checking: 'oompaData'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Formula', 'expm', 'numDeriv', 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'lhs', 'logitnorm', 'nloptr', 'GPfit', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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
Packages required but not available: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Package suggested but not available for checking: 'crossval'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'mvtnorm'

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

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'
'LazyData' is specified without a 'data' directory
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:
  'gamlss', 'gamlss.cens', 'gamlss.dist', 'ineq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dplyr'
Packages required but not available:
  'matrixStats', 'network', 'gplots', 'doParallel', 'foreach', 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'partitions', 'rBeta2009', 'Rcpp', 'Rdpack', 'scales',
  'RcppArmadillo'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rappdirs', 'yaml', 'httr', 'jsonlite', 'xml2', 'assertthat',
  'semver'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'kedd', 'nor1mix', 'fitdistrplus', 'mclust', 'Rdpack',
  'doParallel', 'foreach'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bin_ps: no visible global function definition for 'runif'
bin_ps: no visible global function definition for 'dbinom'
draw_i: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
Packages required but not available:
  'lubridate', 'Rmpfr', 'gmp', 'dplyr', 'stringr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'knitr', 'rmarkdown', 'ggplot2',
  'qpdf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randomForest', 'data.table', 'rlist'

Packages suggested but not available for checking:
  'foreach', 'knitr', 'rmarkdown', 'correlbinom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
IndivdRUMIndMH: no visible global function definition for
  'flush.console'
dRUMAuxMix: no visible global function definition for 'flush.console'
dRUMHAM: no visible global function definition for 'flush.console'
dRUMIndMH: no visible global function definition for 'flush.console'
print.binomlogit: no visible global function definition for 'is'
summary.binomlogit: no visible global function definition for 'is'
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages unavailable to check Rd xrefs: 'mcmc', 'bayesm'
Packages suggested but not available for checking: 'polynom', 'ggplot2'
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  'ggplot2' 'lattice' 'polynom' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' 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
Package required but not available: 'binom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenOrd', 'OrdNor', 'BB', 'corpcor', 'mvtnorm'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'edgeR', 'pracma', 'quadprog', 'Rsamtools', 'GenomicAlignments',
  'GenomicRanges', 'IRanges', 'csaw', 'SummarizedExperiment',
  'BiocGenerics', 'S4Vectors', 'RMySQL'

Packages suggested but not available for checking:
  'nleqslv', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bins.quantiles: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/BinSegBstrap.Rnw'
(Is a VignetteBuilder field missing?)

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

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: 'clinfun'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'discretization', 'Formula', 'testthat', 'BAMMtools', 'earth'
'LazyData' is specified without a 'data' directory
Running examples in 'binst-Ex.R' failed
The error most likely occurred in:

> ### Name: create_breaks
> ### Title: A convenience functon for creating breaks with various methods.
> ### Aliases: create_breaks
> 
> ### ** Examples
> 
> kmeans_breaks <- create_breaks(1:10)
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 1 2 2 2 3 3 3
> 
> # passing the k means parameter "centers" = 4
> kmeans_breaks <- create_breaks(1:10, list(centers=4))
> create_bins(1:10, kmeans_breaks)
 [1] 1 1 1 2 2 2 3 3 3 3
> 
> entropy_breaks <- create_breaks(1:10, rep(c(1,2), each = 5), method="entropy")
Error in create_mdlpbreaks(x, y) : 
  Please install discretization: install.packages('discretization')
Calls: create_breaks -> create_mdlpbreaks
Execution halted
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: 'Rcpp'

Packages suggested but not available for checking:
  'XML', 'RCurl', 'ncdf4', 'igraph', 'bigmemory', 'knitr', 'testthat',
  'httr', 'msa', 'Biostrings'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'moments', 'Rcpp', 'stringr', 'tuneR'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'magrittr', 'nplr', 'reshape2', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'htmlwidgets', 'jsonlite', 'plyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'devtools', 'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Skipping vignette re-building
Packages suggested but not available for checking:
  'BiocVersion', 'remotes', 'rmarkdown', 'testthat', 'withr', 'curl',
  'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'gtools', 'Rcpp', 'rgl', 'e1071', 'randomForest', 'pROC', 'ROCR',
  'arules', 'pamr', 'FSelector', 'RWeka'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'yaml', 'digest', 'uuid', 'jsonvalidate', 'httr', 'curl',
  'crayon', 'cli', 'stringr', 'magrittr', 'rmarkdown'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'vegan3d', 'rgl', 'permute', 'car', 'RODBC', 'effects', 'multcomp',
  'ellipse', 'maptree', 'sp', 'splancs', 'akima', 'dismo', 'raster',
  'rgdal', 'maxlike', 'gbm', 'randomForest', 'gam', 'earth', 'mda',
  'kernlab', 'e1071', 'glmnet', 'bootstrap', 'PresenceAbsence',
  'geosphere', 'maptools', 'ENMeval', 'red', 'rgeos', 'igraph', 'Rlof',
  'maxnet', 'party', 'readxl', 'colorspace', 'dplyr', 'rlang', 'sf',
  'blockCV'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/biogas_quick_start.Rnw'
   'inst/doc/calcBgMan_function.Rnw'
   'inst/doc/calcBgVol_function.Rnw'
   'inst/doc/predBg_function.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/biogas_quick_start.Rnw'
   'vignettes/calcBgMan_function.Rnw'
   'vignettes/calcBgVol_function.Rnw'
   'vignettes/predBg_function.Rnw'
(Is a VignetteBuilder field missing?)
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:
  'raster', 'stringr', 'maptools', 'vegan', 'sp'

Package suggested but not available for checking: 'dismo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'slam', 'combinat', 'entropy', 'partitions'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'tibble', 'dplyr', 'FME', 'rlang', 'purrr', 'ggplot2',
  'cowplot', 'lamW', 'tidyr', 'formula.tools'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'edgeR', 'limma', 'knitr', 'wordcloud', 'RColorBrewer'

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'mice', 'magrittr', 'ggplot2', 'tidyr', 'desc', 'lme4',
  'mitml'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rentrez', 'xml2', 'DBI', 'RMySQL', 'glue', 'memoise'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'fields', 'spatstat.geom', 'spatstat.core', 'spatstat',
  'sp', 'classInt'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'biomaRt', 'Biostrings', 'curl', 'tibble', 'jsonlite', 'data.table',
  'dplyr', 'readr', 'downloader', 'RCurl', 'XML', 'httr', 'stringr',
  'purrr', 'R.utils', 'philentropy', 'fs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'testthat', 'seqinr', 'magrittr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RCurl', 'rjson', 'rcdk', 'Biostrings', 'GOSemSim', 'ChemmineR',
  'fmcsR', 'pls', 'randomForest', 'org.Hs.eg.db'

Packages suggested but not available for checking: 'RUnit', 'BiocGenerics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'raster', 'reshape', 'ggplot2', 'abind', 'rasterVis', 'pROC',
  'gbm', 'mda', 'randomForest', 'PresenceAbsence', 'dismo', 'caret',
  'ENMeval', 'doParallel', 'foreach', 'earth', 'dplyr', 'tidyr',
  'checkmate', 'maxnet', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'ade4', 'Hmisc', 'gam', 'testthat', 'ecospat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'RJSONIO', 'MGRASTer'
'library' or 'require' call to 'MGRASTer' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for 'packageVersion'
biom.matrix: no visible global function definition for 'packageVersion'
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Running 'tests.R'
Running the tests in 'tests/tests.R' failed.
Last 13 lines of output:
  p 116 136 156 176 196
  q 117 137 157 177 197
  r 118 138 158 178 198
  s 119 139 159 179 199
  t 120 140 160 180 200
  
  $comment
  NULL
  
  ======= as.character ===================
  Error in loadNamespace(x) : there is no package called 'RJSONIO'
  Calls: applyBiomMethods ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  In addition: Warning message:
  BIOM.utils: unspecified type defaulting to "OTU table" 
  Execution halted
Packages required but not available:
  'FME', 'bioinactivation', 'corrplot', 'dplyr', 'ggplot2', 'MEIGOR',
  'rlang', 'tidyr', 'tidyverse', 'tidyselect'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dbscan', 'factoextra', 'gplots', 'RColorBrewer'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'curl', 'data.table', 'fields', 'ggmap', 'ggplot2',
  'lubridate', 'lutz', 'raster', 'rgdal', 'rhdf5', 'sp', 'tidyr',
  'viridisLite', 'viridis', 'maptools'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bio3d', 'circular', 'bigmemory', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'amap', 'e1071', 'scales', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vctrs', 'tibble', 'ape', 'crayon', 'dplyr', 'pillar', 'stringr',
  'readr', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pkgconfig', 'cobs', 'corpcor', 'devtools', 'glmnet', 'grplasso',
  'mboost', 'plsRcox', 'pROC', 'PRROC', 'RCurl', 'survAUC'

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

Packages suggested but not available for checking:
  'bshazard', 'rstpm2', 'Epi', 'dplyr'

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

Packages suggested but not available for checking:
  'ggplot2', 'car', 'plotrix', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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.
Packages required but not available:
  'ggplot2', 'magrittr', 'dr4pl', 'tidyverse'

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:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'soilphysics', 'tkrplot', 'rpanel', 'SpatialEpi'
Packages required but not available: 'biomaRt', 'plotrix', 'svglite'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'r2d3', 'purrr', 'dplyr', 'tidyr', 'stringr',
  'tibble', 'downloader'

Packages suggested but not available for checking:
  'knitr', 'bipartite', 'vegan', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vegan', 'sna', 'fields', 'igraph', 'permute'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dendroextras', 'matlib', 'rgl', 'shapes', 'tcltk2', 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colorspace', 'deldir', 'rgl', 'tcltk2', 'tkrplot'

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.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'numDeriv', 'Rcpp', 'Formula', 'optimr', 'pbivnorm', 'mvtnorm',
  'RcppTN', 'coda', 'RcppArmadillo'

Package suggested but not available for checking: 'sampleSelection'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geosphere', 'ks', 'lazyData', 'raster', 'rgdal', 'rgeos',
  'rworldmap', 'rworldxtra', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dbscan', 'dplyr', 'geosphere', 'leaflet', 'lubridate',
  'magrittr', 'rgdal', 'rgeos', 'rlang', 'sf', 'sp', 'stringr',
  'shotGroups', 'taxize', 'tidyr', 'xts', 'zoo'

Packages suggested but not available for checking:
  'covr', 'knitr', 'leaflet.extras', 'leafpm', 'mapedit', 'maps',
  'rgbif', 'rmarkdown', 'shiny', 'testthat', 'vegan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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:
  'classInt', 'dplyr', 'ggplot2', 'glue', 'rlang', 'sf', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown', 'tidyr', 'sirt', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'bisect-Ex.R' failed
The error most likely occurred in:

> ### Name: bisect_semi_suprevised
> ### Title: Add together two numbers.
> ### Aliases: bisect_semi_suprevised
> 
> ### ** Examples
> 
> ## Randomly choose samples to be used as known
> n_known_samples <- 50
> known_samples_indices <- sample.int(nrow(baseline_GSE40279), size = n_known_samples)
> known_samples <- as.matrix(baseline_GSE40279[known_samples_indices, ])
> 
> ## Fit a dirichlet distribution to known samples to use as prior
> fit_dirichlet <- sirt::dirichlet.mle(as.matrix(known_samples))
Error in loadNamespace(x) : there is no package called 'sirt'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'devtools'

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

Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvQuad', 'Rcpp', 'foreach', 'itertools', 'RcppArmadillo',
  'RcppEigen'

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

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

Packages suggested but not available for checking:
  'Seurat', 'plyr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'tidyr', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'phytools', 'coda', 'sm', 'vioplot', 'xml2'

Package suggested but not available for checking: 'mvMORPH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'attempt', 'curl', 'digest', 'dplyr', 'httr', 'jsonlite',
  'lubridate', 'magrittr', 'progress', 'purrr', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'httptest', 'knitr', 'rmarkdown', 'testthat',
  'tidyquant'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown', 'microbenchmark',
  'bit64', 'ff'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Packages unavailable to check Rd xrefs: 'ff', 'bit64'
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: 'diptest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
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:
  'shiny', 'shinyAce', 'rpivotTable', 'corrgram'

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

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

Packages suggested but not available for checking: 'misc3d', 'probhat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'cubature', 'regpro', 'lpSolve', 'mvtnorm', 'copula'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'Rcpp'

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

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

> ### Name: bivrp
> ### Title: Bivariate Residual Plots with Simulation Polygons
> ### Aliases: bivrp print.bivrp
> 
> ### ** Examples
> 
> ## simulating a bivariate normal response variable
> 
> require(mvtnorm)
Loading required package: mvtnorm
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'mvtnorm'
> 
> n <- 40
> beta1 <- c(2, .4)
> beta2 <- c(.2, .2)
> x <- seq(1, 10, length = n)
> X <- model.matrix(~ x)
> mu1 <- X%*%beta1
> mu2 <- X%*%beta2
> sig1 <- 2
> sig2 <- 3
> sig12 <- -1.7
> Sig1 <- diag(rep(sig1), n)
> Sig2 <- diag(rep(sig2), n)
> Sig12 <- diag(rep(sig12), n)
> V <- rbind(cbind(Sig1, Sig12),
+            cbind(Sig12, Sig2))
> 
> set.seed(2016)
> Y <- as.numeric(rmvnorm(1, c(mu1, mu2), V))
Error in rmvnorm(1, c(mu1, mu2), V) : could not find function "rmvnorm"
Execution halted
Packages required but not available: 'BinOrdNonNor', 'rootSolve'

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

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

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

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

Packages suggested but not available for checking:
  'RQuantLib', 'timeDate', 'knitr', 'testthat', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking: 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'numDeriv', 'rcdd', 'geometry', 'proxy', 'spaMM', 'Rcpp', 'nloptr',
  'pbapply', 'foreach', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'minqa', 'lbfgsb3c', 'igraph'

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

Packages suggested but not available for checking:
  'testthat', 'LaF', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'ggExtra'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'ggplot2', 'knitr', 'stringr', 'jmvcore', 'R6', 'rmarkdown'

Package suggested but not available for checking: 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'commonmark', 'curl', 'digest', 'dplyr', 'fs',
  'getPass', 'here', 'htmltools', 'httr', 'jsonlite', 'magrittr',
  'mime', 'rlang', 'rmarkdown', 'stringr', 'uuid'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'glue', 'testthat', 'keyring', 'knitr',
  'spelling', 'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'mnormt', 'R6', 'truncnorm', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Packages required but not available:
  'RGtk2', 'cairoDevice', 'plot3D', 'plot3Drgl', 'rgl', 'network',
  'sna', 'ergm', 'statnet.common', 'haven'

Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lavaan', 'Rcpp', 'RcppParallel', 'MCMCpack', 'coda', 'mnormt',
  'nonnest2', 'loo', 'rstan', 'rstantools', 'bayesplot',
  'future.apply', 'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'runjags', 'modeest', 'rjags', 'semTools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quadprog', 'RUnit', 'timeSeries', 'fBasics', 'fMultivar',
  'fPortfolio', 'rmarkdown', 'knitr'

Packages suggested but not available for checking:
  'sn', 'corpcor', 'mnormt'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'knitcitations'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arm', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'mvtnorm', 'testthat'
'LazyData' is specified without a 'data' directory
Running examples in 'BLModel-Ex.R' failed
The error most likely occurred in:

> ### Name: BL_post_distr
> ### Title: Computes the Black-Litterman posterior distribution.
> ### Aliases: BL_post_distr
> 
> ### ** Examples
> 
> library(mvtnorm)
Error in library(mvtnorm) : there is no package called 'mvtnorm'
Execution halted
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: 'rlang', 'vctrs'

Packages suggested but not available for checking:
  'covr', 'crayon', 'pillar', 'testthat'

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

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'cowplot', 'automap', 'rgeos', 'future',
  'future.apply', 'shiny', 'shinydashboard', 'geosphere', 'rmarkdown',
  'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'PopGenome'

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
blockMessage : <anonymous>: no visible global function definition for
  'head'
blockMessage: no visible global function definition for 'head'
blockMessage: no visible global function definition for 'tail'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'sna', 'doRNG', 'doParallel', 'foreach'
Packages required but not available: 'Rcpp', 'digest', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'pkgdown', 'devtools', 'ggplot2', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking:
  'nbpMatching', 'RItools', 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rmarkdown', 'bookdown', 'knitr', 'htmltools', 'yaml', 'httpuv',
  'later', 'xfun', 'servr'

Packages suggested but not available for checking:
  'testit', 'shiny', 'miniUI', 'stringr', 'rstudioapi', 'processx',
  'whoami'

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

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', 'data.table', 'ggplot2', 'gridExtra', 'lest', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'ineq', 'knitr', 'magrittr', 'rmarkdown', 'testthat',
  'vdiffr', 'xplorerr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'mvQuad', 'numDeriv', 'randtoolbox', 'Formula',
  'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjags', 'mvtnorm', 'openxlsx', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'R6'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable',
  'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable',
  'ggplot2'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'rgl'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'leaps', 'robustbase', 'inline', 'rrcov'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Amelia', 'snowfall', 'lavaan', 'sem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R2jags', 'forestplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'ggplot2', 'forecast', 'loo',
  'Rdpack', 'BH', 'RcppEigen', '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:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'edstan', 'ggplot2',
  'GGUM', 'loo', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'plm'

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

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

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

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

Packages suggested but not available for checking:
  'qgraph', 'knitr', 'rmarkdown', 'reshape2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tensor', 'Rcpp', 'reshape2', 'gtools'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'pixmap', 'testthat'
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: 'xml2', 'rvest'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lpSolve', 'LowRankQP', 'matrixStats', 'Rcpp'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'xml2', 'stringr', 'tibble', 'readr'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'ggplot2', 'dplyr', 'tidyr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'reshape2', 'gridExtra', 'loo', 'mcmcse', 'bridgesampling',
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Brobdingnag', 'MCMCpack', 'expm', 'ks', 'mvtnorm', 'doParallel',
  'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BGLR', 'doSNOW', 'dplyr', 'foreach', 'matrixcalc', 'mvtnorm',
  'progress', 'snow', 'tidyr', 'Rcpp', 'RcppArmadillo'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'entropy', 'matrixStats', 'Rcpp', 'BH'

Packages suggested but not available for checking:
  'graph', 'gRain', 'gRbase', 'mlr', 'testthat', 'knitr',
  'ParamHelpers', 'Rgraphviz', 'rmarkdown', 'mlbench', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'bnlearn'
Malformed Description field: should contain one or more complete sentences.
make_topology: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'igraph', 'gRain', 'ROCR', 'Rmpfr', 'gmp'
Running examples in 'bnlearn-Ex.R' failed
The error most likely occurred in:

> ### Name: arc.strength
> ### Title: Measure arc strength
> ### Aliases: arc.strength boot.strength custom.strength bf.strength
> ###   averaged.network mean.bn.strength
> ### Keywords: network scores independence tests structure learning
> 
> ### ** Examples
> 
> data(learning.test)
> res = gs(learning.test)
> res = set.arc(res, "A", "B")
> arc.strength(res, learning.test)
  from to      strength
1    A  B  0.000000e+00
2    A  D  0.000000e+00
3    B  E 1.024198e-320
4    C  D  0.000000e+00
5    F  E 3.935648e-245
> 
> ## Not run: 
> ##D arcs = boot.strength(learning.test, algorithm = "hc")
> ##D arcs[(arcs$strength > 0.85) & (arcs$direction >= 0.5), ]
> ##D averaged.network(arcs)
> ##D 
> ##D start = random.graph(nodes = names(learning.test), num = 50)
> ##D netlist = lapply(start, function(net) {
> ##D   hc(learning.test, score = "bde", iss = 10, start = net) })
> ##D arcs = custom.strength(netlist, nodes = names(learning.test),
> ##D          cpdag = FALSE)
> ##D arcs[(arcs$strength > 0.85) & (arcs$direction >= 0.5), ]
> ##D modelstring(averaged.network(arcs))
> ## End(Not run)
> 
> bf.strength(res, learning.test, score = "bds", prior = "marginal")
Loading required namespace: Rmpfr
Failed with error:  'there is no package called 'Rmpfr''
Error in check.and.load.package("Rmpfr") : 
  this function requires the Rmpfr package.
Calls: bf.strength -> check.and.load.package
Execution halted
Packages required but not available: 'rjags', 'coda', 'ggplot2', 'igraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bnlearn', 'DiagrammeR', 'dplyr', 'ggplot2', 'gRain', 'gRbase',
  'gridExtra', 'matrixcalc', 'purrr', 'RColorBrewer', 'reshape2',
  'rlang', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

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

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: 'car', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bnlearn', 'fastDummies', 'lavaan', 'Rgraphviz', 'semPlot', 'xlsx'

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

Packages suggested but not available for checking:
  'GreedyEPL', 'Rmpfr', 'gmp', 'knitr', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gplots', 'matrixcalc', 'mvtnorm', 'plyr', 'Rcpp', 'truncnorm',
  'RcppArmadillo'

Package suggested but not available for checking: 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'coda', 'Rcpp', 'ggpubr', 'RcppArmadillo', 'RcppDist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'popkin', 'testthat', 'knitr', 'rmarkdown', 'RColorBrewer'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bnlearn', 'corpcor', 'glmnet', 'graph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'rgdal', 'sf', 'gRbase', 'gRain', 'doParallel', 'foreach'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'ggplot2', 'plot3D', 'threejs', 'gridExtra', 'cubature',
  'Formula', 'plyr', 'corrplot', 'label.switching'

Packages suggested but not available for checking: 'mvtnorm', 'np'

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

Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'qgraph', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/bnstruct.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'visNetwork', 'bnlearn', 'igraph', 'shiny', 'assertthat', 'caret',
  'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'cytofan', 'dplyr', 'reshape2', 'RColorBrewer', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'hash', 'DIME'

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

Package suggested but not available for checking: 'RCurl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'tidyr', 'tidyselect', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'crul', 'stringr', 'jsonlite', 'reshape', 'plyr',
  'data.table', 'tibble'

Packages suggested but not available for checking:
  'sangerseqR', 'knitr', 'testthat', 'vcr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'mvtnorm'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'bnstruct'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'crayon', 'data.table', 'dplyr', 'httr', 'hoardr', 'janitor',
  'jsonlite', 'lubridate', 'magick', 'magrittr', 'readr', 'rvest',
  'terra', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'ASGS.foyer', 'covr', 'testthat', 'knitr', 'rmarkdown', 'ggplot2',
  'ggthemes', 'gridExtra', 'maps', 'mapproj', 'rappdirs', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bookdown', 'xaringan', 'magick', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'knitr', 'rmarkdown', 'xfun', 'tinytex', 'yaml'

Packages suggested but not available for checking:
  'bslib', 'downlit', 'htmlwidgets', 'jsonlite', 'rstudioapi',
  'miniUI', 'rsconnect', 'servr', 'shiny', 'tibble', 'testit', 'tufte',
  'xml2', 'webshot'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Package unavailable to check Rd xrefs: 'testthat'
GNU make is a SystemRequirements.
Package required but not available: 'Boom'

Packages suggested but not available for checking:
  'testthat', 'mlbench', 'igraph'

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

Package suggested but not available for checking: 'mlbench'

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

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

Packages suggested but not available for checking:
  'knitr', 'xtable', 'mlbench', 'e1071', 'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package unavailable to check Rd xrefs: 'HDInterval'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'metafor', 'pbmcapply', 'HSAUR3', 'knitr', 'rmarkdown'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'testthat'

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

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', 'igraph', 'IsingFit', 'qgraph', 'dplyr', 'tidyr',
  'gtools', 'corpcor', 'IsingSampler', 'mvtnorm', 'abind', 'huge',
  'mgm', 'relaimpo', 'NetworkToolbox', 'pbapply', 'graphicalVAR',
  'BDgraph', 'psychTools', 'networktools', 'lavaan', 'glasso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
specdens: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
boot.stepAIC: no visible global function definition for 'update'
boot.stepAIC: no visible binding for global variable 'coef'
boot.stepAIC : <anonymous>: no visible global function definition for
  'anova'
boot.stepAIC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'sampling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MatrixEQTL', 'foreach', 'data.table'

Packages suggested but not available for checking:
  'doMC', 'doParallel', 'qvalue', 'testthat'

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

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'abind', 'corpcor', 'fishMod', 'lifecycle', 'mvtnorm',
  'R2jags', 'reshape2'

Packages suggested but not available for checking: 'mvabund', 'corrplot'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'mlbench', 'rFerns', 'randomForest', 'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'RSQLite', 'jsonlite', 'phangorn', 'plotrix'

Packages suggested but not available for checking:
  'prettydoc', 'knitr', 'rmarkdown', 'XML', 'rentrez', 'httr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'devtools', 'ISLR', 'kableExtra', 'knitr', 'rmarkdown', 'sparsenet'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'covr', 'digest'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'latticeExtra', 'hexbin', 'gridExtra', 'gtable', 'e1071'

Packages suggested but not available for checking:
  'Cairo', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/PlottingGuide.Rnw'
(Is a VignetteBuilder field missing?)

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

Packages suggested but not available for checking: 'mdscore', 'flexmix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'R6', 'rlang', 'roxygen2', 'shiny',
  'testthat'

Package which this enhances but not available for checking: 'rstudioapi'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'assertthat', 'bit64', 'dplyr', 'digest', 'fs', 'glue', 'httr',
  'httpuv', 'magrittr', 'mime', 'purrr', 'rio', 'rlang', 'stringr',
  'tibble', 'lifecycle', 'jsonlite'

Packages suggested but not available for checking:
  'clipr', 'conflicted', 'gargle', 'here', 'jose', 'knitr', 'openssl',
  'png', 'rmarkdown', 'sodium', 'testthat', 'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'knitr', 'rmarkdown', 'tidyr', 'shiny'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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: 'scatterplot3d', 'rgl', 'xtable'

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.
Packages required but not available:
  'coda', 'dplyr', 'tidyr', 'stringr', 'ggplot2', 'gtools', 'Rcpp',
  'RcppParallel', 'rstan', 'rstantools', 'tibble', 'tidyselect',
  'HDInterval', 'shinystan', 'loo', 'magrittr', 'badger', 'rlang',
  'knitr', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr', 'bayesplot', 'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bPeaksAnalysis: no visible global function definition for 'write.table'
dataReading: no visible global function definition for 'read.table'
dataSmoothing: no visible global function definition for 'filter'
peakDetection: no visible global function definition for 'quantile'
peakDetection: no visible global function definition for 'pdf'
peakDetection: no visible global function definition for 'par'
peakDetection: no visible global function definition for 'text'
peakDetection: no visible global function definition for 'abline'
peakDetection: no visible global function definition for 'points'
peakDetection: no visible global function definition for 'dev.off'
peakDetection: no visible global function definition for 'write.table'
peakDrawing: no visible global function definition for 'par'
peakDrawing: no visible global function definition for 'abline'
peakLocation: no visible global function definition for 'read.table'
peakLocation: no visible global function definition for 'pdf'
peakLocation: no visible global function definition for 'barplot'
peakLocation: no visible global function definition for 'dev.off'
peakLocation: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline barplot dev.off filter par pdf points quantile read.table text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'igraph', 'mvtnorm', 'maptools', 'sp', 'phytools',
  'fields', 'coda', 'OpenStreetMap', 'ggmap', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mcmcse', 'pgmm', 'mvtnorm', 'Rcpp', 'gtools', 'label.switching',
  'fabMix', 'mclust', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'haven', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'qpdf', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'lubridate', 'ggplot2', 'gridExtra', 'cowplot',
  'tibble', 'tidyselect', 'gtable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'png'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pracma', 'GIGrvg', 'truncnorm', 'NPflow', 'invgamma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'geojsonio', 'jsonlite', 'maptools', 'plotfunctions',
  'raster', 'rgbif', 'rgeos', 'rworldmap', 'sp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'brglm', 'gtools', 'lme4', 'qvcalc'

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

Package which this enhances but not available for checking: 'gnm'

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

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', 'braidrm'

Packages suggested but not available for checking: 'gtable', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'abind', 'data.table', 'doParallel', 'foreach', 'permute'

Packages suggested but not available for checking:
  'Hmisc', 'RGtk2', 'ade4', 'cairoDevice', 'car', 'expm', 'ggplot2',
  'ggrepel', 'gridExtra', 'mediation', 'oro.nifti', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CCA', 'kernlab', 'elasticnet', 'rgl', 'brainR', 'misc3d',
  'oro.nifti', 'knitr'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'misc3d', 'oro.nifti'

Package suggested but not available for checking: 'servr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'data.table'

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Imap'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'e1071', 'kernlab', 'xgboost', 'caret',
  'randomForest', 'DALEX', 'ranger', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'ggfittext', 'ggplot2', 'broom', 'multcomp',
  'purrr', 'readr', 'readxl', 'signal', 'stringr', 'tibble', 'tidyr',
  'xml2'

Packages suggested but not available for checking:
  'gridExtra', 'knitr', 'rmarkdown', 'testthat', 'breathteststan',
  'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'purrr', 'rstan', 'rstantools', 'stringr', 'tibble',
  'tidyr', 'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'ggplot2', 'shinystan', 'bayesplot', 'testthat', 'covr', 'knitr',
  'rmarkdown', 'breathtestcore'

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

Packages suggested but not available for checking:
  'RColorBrewer', 'RgoogleMaps', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'enrichwith', 'lpSolveAPI', 'numDeriv'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'magrittr', 'dplyr', 'tidyr', 'purrr', 'scales', 'farver',
  'colorspace', 'rgl'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gridExtra', 'png', 'jpeg', 'tibble', 'raster',
  'stringr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'reshape2', 'ggplot2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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:
  'data.table', 'ggplot2', 'shiny', 'shinydashboard', 'plotly', 'BSDA',
  'outliers'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'Brobdingnag', 'stringr', 'coda', 'scales'

Packages suggested but not available for checking:
  'testthat', 'Rcpp', 'RcppEigen', 'R2jags', 'rjags', 'runjags',
  'knitr', 'rmarkdown', 'R.rsp', 'BayesFactor', 'rstan', 'rstanarm',
  'nimble', 'MCMCpack'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridExtra', 'rmarkdown', 'glue', 'pander', 'lubridate',
  'tibble', 'sm', 'RColorBrewer', 'forcats', 'GGally'

Packages suggested but not available for checking:
  'knitr', 'hexbin', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
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:
  'magrittr', 'dplyr', 'httr', 'jsonlite', '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:
  'RANN', 'rdist', 'matrixStats', 'pbapply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deldir', 'deSolve', 'fasterize', 'fftwtools', 'mvtnorm', 'raster',
  'Rcpp', 'rgdal', 'rgeos', 'sf', 'sp', 'testthat', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown', 'dplyr', 'testthat', 'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'
Packages required but not available:
  'Rcpp', 'rstan', 'ggplot2', 'loo', 'rstantools', 'bayesplot',
  'shinystan', 'projpred', 'bridgesampling', 'glue', 'future',
  'matrixStats', 'nleqslv', 'coda', 'abind', 'backports'

Packages suggested but not available for checking:
  'testthat', 'emmeans', 'cmdstanr', 'RWiener', 'rtdists', 'mice',
  'spdep', 'mnormt', 'lme4', 'MCMCglmm', 'splines2', 'ape', 'arm',
  'statmod', 'digest', 'diffobj', 'R.rsp', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'lme4', 'matrixsampling', 'rlang', 'tidyr'

Packages suggested but not available for checking:
  'AGD', 'ggplot2', 'gridExtra', 'knitr', 'mice', 'mvtnorm', 'plyr',
  'svglite', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'RPushbullet', 'jsonlite', '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', 'magrittr', 'parameters',
  'performance', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'generics', 'lavaan', 'lme4', 'rmarkdown', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cli', 'dplyr', 'labelled', 'lifecycle', 'purrr', 'rlang',
  'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'cmprsk', 'covr', 'emmeans', 'lfe', 'forcats',
  'gam', 'gee', 'geepack', 'ggplot2', 'glue', 'gt', 'gtsummary',
  'knitr', 'lavaan', 'lme4', 'mice', 'ordinal', 'parameters',
  'rmarkdown', 'rstanarm', 'spelling', 'survey', 'testthat', 'VGAM'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'tidyr', 'plyr', 'purrr', 'tibble', 'reshape2',
  'stringr', 'coda', 'TMB', 'cubelyr'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'ggplot2', 'MCMCglmm', 'lme4', 'brms', 'gamlss',
  'gamlss.data', 'lmerTest', 'pbkrtest', 'glmmADMB', 'glmmTMB',
  'dotwhisker', 'pander', 'R2jags', 'GLMMadaptive', 'rstan', 'rstanarm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'dplyr', 'ellipsis', 'generics', 'glue', 'purrr',
  'rlang', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'AER', 'akima', 'AUC', 'bbmle', 'betareg', 'biglm', 'binGroup',
  'btergm', 'car', 'caret', 'cmprsk', 'coda', 'covr', 'drc', 'e1071',
  'emmeans', 'epiR', 'ergm', 'fixest', 'gam', 'gee', 'geepack',
  'ggplot2', 'glmnet', 'glmnetUtils', 'gmm', 'Hmisc', 'irlba',
  'joineRML', 'Kendall', 'knitr', 'ks', 'Lahman', 'lavaan', 'leaps',
  'lfe', 'lm.beta', 'lme4', 'lmodel2', 'lmtest', 'lsmeans', 'maps',
  'maptools', 'margins', 'mclust', 'mediation', 'metafor', 'mfx',
  'mlogit', 'modeldata', 'modeltests', 'muhaz', 'multcomp', 'network',
  'orcutt', 'ordinal', 'plm', 'poLCA', 'psych', 'quantreg', 'Rchoice',
  'rgeos', 'rmarkdown', 'robust', 'robustbase', 'rsample', 'sandwich',
  'sp', 'spdep', 'spatialreg', 'speedglm', 'spelling', 'survey',
  'systemfit', 'testthat', 'tseries', 'vars', 'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'spelling', 'knitr', 'R.rsp', 'microbenchmark', 'rmarkdown',
  'ggplot2'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'
Running 'spelling.R'
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'RCurl', 'jsonlite', 'httpuv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'curl', 'ape', 'taxize', 'phytools', 'phylocomr',
  'conditionz'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gsl', 'SuppDists', 'TeachingDemos', 'hypergeo', 'pander', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'R.rsp', 'magrittr'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pacman', 'jmv', 'mediation', 'interactions', 'MuMIn', 'performance',
  'texreg', 'cowplot', 'see', 'glue', 'crayon', 'ggplot2', 'ggtext'

Packages suggested but not available for checking:
  'rstudioapi', 'rio', 'dplyr', 'tidyr', 'stringr', 'forcats',
  'data.table', 'car', 'psych', 'afex', 'emmeans', 'effectsize',
  'jtools', 'lavaan', 'lmtest', 'lme4', 'lmerTest', 'GGally'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DiffBind', 'Rsamtools', 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'MCMCpack', 'GPArotation', 'TeachingDemos', 'blavaan', 'blme',
  'rstan'

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

Packages suggested but not available for checking:
  'plotly', 'shinyWidgets', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gamlss', 'multcomp', 'MCPAN', 'mvtnorm', 'mratios'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjags', 'coda', 'dplyr', 'ggplot2', 'gridExtra', 'msm', 'mvtnorm',
  'rworldxtra', 'sp', 'tibble', 'lubridate'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'sf', 'surveillance', 'spdep',
  'RColorBrewer', 'deldir'

VignetteBuilder package required for checking but not installed: 'knitr'

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

> ### Name: bscaling-package
> ### Title: Binary Scaling
> ### Aliases: bscaling
> 
> ### ** Examples
> 
> dt = c(5,3,6,9,4)
> ## When the variable to be scaled is a single-variable data frame object use: 
> ## data.frame name[[1]], or diffrent subscript otherwise to get the vector for sc01
> ## cutoff value = 5
> bvar = sc01(dt, 5)
Error in assign("indc", NULL, envir = .BaseNamespaceEnv) : 
  cannot add binding of 'indc' to the base environment
Calls: sc01 -> assign
Execution halted
Package required but not available: 'e1071'

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'magrittr', 'viridis', 'visNetwork', 'shiny', 'Rcpp',
  'rstan', 'rstantools', 'DiagrammeR', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'knitr', 'devtools', 'roxygen2', 'testthat', 'covr', 'rmarkdown',
  'bayesplot', 'tidybayes', 'ggplot2', 'gridExtra', 'shinythemes',
  'ggfortify', 'shinyjs', 'shinycssloaders', 'plotly', 'ggridges',
  'fmsb', 'visdat', 'DT', 'tidyr', 'dplyr', 'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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 required but not available:
  'intrval', 'mefa4', 'deldir', 'pbapply'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'detect', 'shiny'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'jsonlite', 'sass', 'digest', 'jquerylib', 'rlang',
  'magrittr'

Packages suggested but not available for checking:
  'shiny', 'rmarkdown', 'knitr', 'testthat', 'withr', 'rappdirs',
  'curl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plot.bspec: no visible global function definition for 'par'
plot.bspec: no visible global function definition for 'matlines'
plot.bspec: no visible global function definition for 'points'
plot.bspec: no visible global function definition for 'axis'
plot.bspec: no visible global function definition for 'mtext'
plot.bspec: no visible global function definition for 'axTicks'
plot.bspec: no visible global function definition for 'box'
plot.bspecACF: no visible global function definition for 'abline'
plot.bspecACF: no visible global function definition for 'matlines'
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "points")
to your NAMESPACE file.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'magrittr', 'purrr', 'lubridate', 'stringr',
  'rmarkdown', 'glue', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'shiny', 'covr', 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'diagis', 'Rcpp', 'RcppArmadillo', 'ramcmc', 'sitmo'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'Hmisc', 'KFAS', 'knitr', 'ramcmc', 'rmarkdown',
  'sde', 'sitmo', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sn', 'ssmn', 'mvtnorm', 'ClusterR'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'html5'

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

Packages suggested but not available for checking:
  'hdi', 'pROC', 'R.rsp', 'knitr', 'gdata'

VignetteBuilder packages required for checking but not installed:
  'R.rsp', 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/cancer.Rnw'
   'inst/doc/mcl.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BoomSpikeSlab', 'zoo', 'xts', 'Boom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GlobalOptions', 'GetoptLong', 'digest', 'clisymbols', 'crayon'

Packages suggested but not available for checking:
  'knitr', 'ssh', 'DT', 'shiny', 'shinyjqui', 'igraph', 'graph',
  'Rgraphviz', 'ggplot2', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'sp', 'sf', 'RcppParallel', 'BH', 'RcppArmadillo'

Package suggested but not available for checking: 'cartography'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xergm.common', 'ggplot2', 'network', 'sna', 'ergm', 'coda', 'ROCR',
  'speedglm', 'igraph', 'RSiena', 'statnet.common'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TeachingDemos', 'Rcpp', 'stringr', 'psychotools', 'RcppArmadillo'

Package suggested but not available for checking: 'gvcm.cat'

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

Packages suggested but not available for checking: 'udpipe', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'actuar', 'coda', 'data.table', 'ggplot2', 'ggforce', 'gridExtra',
  'plyr', 'reshape2', 'R2jags', 'scales'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'BTYD', 'coda', 'data.table', 'mvtnorm', 'bayesm'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'gsl', 'lintr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/BTYD-walkthrough.Rnw'
(Is a VignetteBuilder field missing?)

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'Amelia', 'mice'

Packages which this enhances but not available for checking:
  'texreg', 'stargazer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'plyr', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 required but not available: 'lme4', 'plyr'

Packages suggested but not available for checking:
  'GLMMadaptive', 'gamm4', 'glmertree', 'glmmTMB', 'knitr', 'lmerTest',
  'ordinal', 'partykit', 'pbkrtest', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstudioapi', 'usethis', 'readr', 'glue', 'stringr', 'magrittr',
  'tibble'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mda', 'mpath', 'mboost', 'gbm', 'earth', 'elasticnet', 'rms',
  'modeltools', 'bst'

Packages suggested but not available for checking:
  'TH.data', 'R.rsp', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'zoo', 'ggplot2', 'plyr', 'dplyr', 'reshape2', 'plotly',
  'robustbase', 'smoother'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tm', 'NLP', 'topicmodels', 'slam'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'car', 'rsq'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'zoo'
Packages required but not available:
  'magrittr', 'dplyr', 'data.table', 'shiny', 'miniUI', 'purrr',
  'tidyr', 'glue', 'forcats', 'rlang', 'eventdataR', 'stringr',
  'lubridate'

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', 'plyr', 'reshape2', 'rlang', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
alpha.proxy: no visible global function definition for 'filled.contour'
alpha.proxy: no visible global function definition for 'axis'
alpha.proxy: no visible global function definition for 'contour'
factor.model.stat: no visible global function definition for 'quantile'
factor.model.stat: no visible global function definition for 'lsfit'
partial.rainbow: no visible binding for global variable 'rainbow'
var.shrink.eqcor: no visible global function definition for 'var'
var.shrink.eqcor: no visible global function definition for 'quantile'
var.shrink.eqcor: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
Package suggested but not available for checking: 'testthat'
Packages unavailable to check Rd xrefs: 'Hmisc', 'gtools', 'testthat'
'LazyData' is specified without a 'data' directory
plot.bursts: no visible global function definition for 'axis'
plot.bursts: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
Package required but not available: 'lubridate'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fs', 'lobstr', 'purrr', 'rlang', 'tibble', 'usethis'

Packages suggested but not available for checking:
  'C50', 'caret', 'clisymbols', 'covr', 'ddalpha', 'dimRed', 'dplyr',
  'e1071', 'earth', 'fastICA', 'flexsurv', 'ipred', 'kernlab', 'kknn',
  'knitr', 'mda', 'modeldata', 'NMF', 'parsnip', 'pkgload', 'pls',
  'QSARdata', 'randomForest', 'ranger', 'RANN', 'recipes', 'rmarkdown',
  'rsample', 'RSpectra', 'testthat', 'TH.data', 'xgboost'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'data.table', 'doParallel', 'foreach', 'ggplot2', 'lava',
  'prodlim', 'RcppArmadillo'

Packages suggested but not available for checking:
  'cvAUC', 'pbapply', 'pROC', 'R.rsp', 'riskRegression', 'testthat'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

Packages suggested but not available for checking:
  'coda', 'vars', 'tinytest'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages unavailable to check Rd xrefs: 'quadprog', 'nnls'
Packages required but not available: 'deSolve', 'rootSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'RcppArmadillo', 'RcppEigen',
  'RcppNumerical'

Package suggested but not available for checking: 'doMPI'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rrBLUP', 'BGLR', 'glmnet', 'randomForest', 'brnn', 'e1071'

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

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

Package suggested but not available for checking: 'testthat'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'data.table', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'mlegp', 'tgp', 'peperr', 'penalizedSVM'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'e1071'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'data.table', 'lazyeval', 'htmlwidgets', 'dplyr',
  'viridis'

Packages suggested but not available for checking:
  'testthat', 'RColorBrewer', 'knitr', 'rmarkdown', 'purrr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partykit', 'RColorBrewer', 'gridExtra', 'ggplot2', 'igraph',
  'reshape2', 'qgraph', 'plyr'

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

Packages suggested but not available for checking: 'knitr', 'modeldata'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggforce', 'gridExtra', 'ggrepel', 'multichull', 'ggplot2', 'plotly',
  'checkmate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'glue', 'rstudioapi', 'crayon', 'fs', 'stringr', 'git2r',
  'cli', 'renv'

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

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

Package suggested but not available for checking: 'ellipse'

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dynlm', 'sandwich', 'tseries', 'urca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'JGR', 'rJava', 'XML', 'bio.infer', 'gdata', 'gmodels', 'quantreg',
  'JavaGD', 'car'

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

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'RLRsim', 'mvtnorm'

Package suggested but not available for checking: 'gamm4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ca', 'classInt', 'FactoMineR', 'ggplot2', 'ggrepel', 'Hmisc',
  'RcmdrMisc', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'cairoDevice/R/zzz.R':
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Package unavailable to check Rd xrefs: 'RGtk2'
Package suggested but not available for checking: 'png'

Package which this enhances but not available for checking: 'FastRWeb'
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.
Packages required but not available:
  'assertthat', 'pbmcapply', 'ggplot2', 'gridExtra'

Packages suggested but not available for checking:
  'MOEADr', 'smoof', 'knitr', 'rmarkdown', 'car', 'dplyr', 'pkgdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'cubature', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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: 'wavethresh', 'LS2W', 'dualtrees'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Package suggested but not available for checking: 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GPfit', 'gelnet', 'kernlab', 'randtoolbox'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'pROC', 'reshape2', 'foreach', 'fitdistrplus',
  'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ncdf4', 'ggplot2', 'lubridate', 'raster', 'rworldmap'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'processx', 'R6'

Packages suggested but not available for checking:
  'cli', 'covr', 'ps', 'rprojroot', 'spelling', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.utils', 'aroma.core', 'R.methodsS3', 'R.oo', 'matrixStats',
  'R.filesets'

Package suggested but not available for checking: 'DNAcopy'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

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', 'fs', 'ggplot2', 'glue', 'httr', 'lubridate', 'magrittr',
  'purrr', 'readr', 'rlang', 'scales', 'stringdist', 'stringr',
  'tibble'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling', 'testthat', 'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'xml2'

Packages suggested but not available for checking:
  'ncdf4', 'roxygen2', 'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sp', 'overlap', 'secr', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'lubridate', 'raster', 'rgdal', 'ritis', 'rmarkdown',
  'taxize', 'testthat', 'tibble', 'unmarked', 'zip', 'RSQLite'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'leaflet', 'mapdeck', 'rmarkdown', 'readr',
  'rgdal', 'rgeos', 'scales', 'sp', 'sf', 'geojsonsf', 'tidyr',
  'lwgeom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'systemfit', 'qvalue', 'reshape2', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'biogram', 'devtools', 'pbapply', 'ranger', 'shiny', 'stringi',
  'dplyr'

Packages suggested but not available for checking:
  'DT', 'ggplot2', 'pander', 'rmarkdown', 'shinythemes', 'spelling'

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

Packages suggested but not available for checking:
  'GenomicRanges', 'IRanges', 'S4Vectors'

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

Packages suggested but not available for checking:
  'rgl', 'corrplot', 'knitr', 'rmarkdown', 'rpart.plot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'fields', 'pheatmap', 'scatterplot3d'

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

Packages suggested but not available for checking:
  'CHNOSZ', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'reshape2', 'Hmisc', 'downloader'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'httr', 'readr', 'rlang', 'xml2', 'rvest', 'stringr',
  'purrr', 'tibble', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scales', 'tidyr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'shiny', 'canvasXpress.data', 'knitr', 'rmarkdown', 'testthat',
  'covr', 'webshot', 'png', 'limma', 'glue', 'dplyr', 'tibble', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'caTools', 'corpcor', 'doParallel', 'evd', 'foreach',
  'here', 'igraph', 'pheatmap', 'propagate', 'qtl', 'qtl2',
  'qtl2convert', 'R6', 'RColorBrewer', 'regress', 'shape', 'stringr',
  'yaml'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'magrittr', 'readxl', 'writexl'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'FME', 'survey', 'ggplot2', 'dplyr', 'tidyr', 'magrittr',
  'circlize', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'htmltools', 'shinyjs', 'shinyWidgets', 'shinydashboard',
  'shinydashboardPlus', 'shinyjqui', 'plotly', 'rintrojs',
  'shinycssloaders', 'visNetwork', 'purrr', 'DT', 'magrittr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'curl', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bootstrapCapwire: no visible global function definition for 'quantile'
drawCapRatesBeta : <anonymous>: no visible global function definition
  for 'rbeta'
drawCapRatesExp : <anonymous>: no visible global function definition
  for 'rexp'
drawCapRatesGamma : <anonymous>: no visible global function definition
  for 'rgamma'
drawCapRatesGeom : <anonymous>: no visible global function definition
  for 'rgeom'
drawCapRatesUnif : <anonymous>: no visible global function definition
  for 'runif'
partitionCountData : find.3.way.partitions: no visible global function
  definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
Packages required but not available: 'reticulate', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'markdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'CARBayesdata', 'coda', 'dplyr', 'GGally', 'leaflet',
  'matrixcalc', 'MCMCpack', 'rgdal', 'sp', 'spam', 'spdep', 'truncnorm'

Packages suggested but not available for checking:
  'deldir', 'maptools', 'shapefiles'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'CARBayesdata', 'coda', 'dplyr', 'GGally', 'ggplot2',
  'gridExtra', 'gtools', 'leaflet', 'matrixcalc', 'matrixStats',
  'MCMCpack', 'rgdal', 'sp', 'spam', 'spdep', 'testthat', 'truncdist',
  'truncnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clipr', 'details', 'httr', 'magick', 'R6', 'RSelenium', 'rtweet',
  'wdman', 'yaml'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'expm', 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rgl', 'vcd'
Package unavailable to check Rd xrefs: 'car'
Package required but not available: 'pastecs'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'lutz', 'magrittr', 'ggplot2', 'tidyr', 'dplyr', 'purrr',
  'tibble', 'readr', 'lubridate', 'stringr', 'rlang', 'broom',
  'hardhat', 'recipes', 'data.table', 'Hmisc', 'generics', 'ggrepel'

Packages suggested but not available for checking:
  'kableExtra', 'plyr', 'stargazer', 'knitr', 'rmarkdown', 'covr',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for 'qnorm'
as.record: no visible global function definition for 'capture.output'
estN: no visible global function definition for 'sd'
estN: no visible global function definition for 'qnorm'
estN.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages required but not available: 'httr', 'jsonlite', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'dplyr', 'ggplot2',
  'spelling', 'RColorBrewer'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'crossval'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pbapply', 'ggplot2', 'digest', 'plyr', 'gridExtra', 'data.table',
  'caret'

Packages suggested but not available for checking:
  'caTools', 'testthat', 'lintr', 'randomForest', 'glmnet', 'kernlab',
  'e1071', 'ipred', 'pROC', 'knitr', 'mlbench', 'gbm', 'klaR',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'foreach', 'plyr', 'ModelMetrics', 'reshape2', 'recipes',
  'withr', 'pROC'

Packages suggested but not available for checking:
  'BradleyTerry2', 'e1071', 'earth', 'fastICA', 'gam', 'ipred',
  'kernlab', 'knitr', 'klaR', 'ellipse', 'mda', 'mlbench', 'MLmetrics',
  'party', 'pls', 'proxy', 'randomForest', 'RANN', 'spls', 'subselect',
  'pamr', 'superpc', 'Cubist', 'testthat', 'dplyr', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'DEoptim', 'pracma', 'truncnorm', 'invgamma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
abundance: no visible global function definition for 'D'
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
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
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
barplotEQR: no visible global function definition for 'barplot'
barplotEQR: no visible global function definition for 'abline'
barplotEQR: no visible global function definition for 'par'
barplotEQR: no visible global function definition for 'text'
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
Packages suggested but not available for checking: 'gsl', 'testthat'
'LazyData' is specified without a 'data' directory
Running examples in 'Carlson-Ex.R' failed
The error most likely occurred in:

> ### Name: Carlson_RC
> ### Title: Carlson elliptic integral RC
> ### Aliases: Carlson_RC
> 
> ### ** Examples
> 
> Carlson_RC(5, 2)
[1] 0.595663+0i
> gsl::ellint_RC(5, 2)
Error in loadNamespace(x) : there is no package called 'gsl'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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: 'quantreg', 'RColorBrewer'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'sm', 'RSQLite'
'library' or 'require' calls in package code:
  'MASS' 'RSQLite' 'grid' 'sm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages unavailable to check Rd xrefs: 'DBI', 'gplots', 'limma', 'sm'
Running examples in 'caroline-Ex.R' failed
The error most likely occurred in:

> ### Name: bestBy
> ### Title: Find the "best" record within subgroups of a dataframe.
> ### Aliases: bestBy
> 
> ### ** Examples
> 
> 
> blast.results <- data.frame(score=c(1,2,34,4,5,3,23), 
+                             query=c('z','x','y','z','x','y','z'), 
+                             target=c('a','b','c','d','e','f','g')
+                             )
> best.hits.R <- bestBy(blast.results, by='query', best='score', inverse=TRUE)
> best.hits.R
  score query target
y    34     y      c
z    23     z      g
x     5     x      e
> ## or using SQLite
> best.hits.sql <- bestBy(blast.results, by='query', best='score', inverse=TRUE, sql=TRUE)
Loading required package: RSQLite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'RSQLite'
Error in dbConnect(dbDriver("SQLite"), dbname = tmpfile) : 
  could not find function "dbConnect"
Calls: bestBy
Execution halted
Packages required but not available:
  'dplyr', 'magrittr', 'tidyr', 'pander', 'lazyeval', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rmarkdown', 'VennDiagram', 'DESeq2', 'sm', 'biomaRt', 'seqinr',
  'scatterplot3d', 'xlsx'

Packages suggested but not available for checking:
  'BiocGenerics', 'knitr', 'stringi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'carData', 'abind', 'pbkrtest', 'quantreg', 'maptools', 'rio', 'lme4'

Packages suggested but not available for checking:
  'alr4', 'coxme', 'knitr', 'leaps', 'lmtest', 'MatrixModels', 'rgl',
  'sandwich', 'SparseM', 'survey'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'corpcor', 'mboost', 'fdrtool'

Packages suggested but not available for checking:
  'microbenchmark', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'maptools', 'plotly', 'rgeos', 'reshape2',
  'rlang', 'sp', 'sf', 'igraph'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'cartography'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'rgeos', 'sp', 'rgdal', 'maptools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'classInt', 'curl', 'png', 'raster', 'Rcpp', 'rgeos', 'sf',
  'slippymath', 'sp'

Packages suggested but not available for checking:
  'lwgeom', 'SpatialPosition', 'knitr', 'rmarkdown', 'rgdal',
  'tinytest', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'animation', 'devtools', 'dplyr', 'gapminder', 'ggplot2', 'knitr',
  'rlist', 'rmarkdown', 'roxygen2', 'sde', 'shiny', 'tidyverse',
  'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tmvtnorm', 'mvtnorm', 'matrixStats', 'xts', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'animation', 'igraph', 'lars', 'limma', 'magic', 'nnls',
  'tnet', 'VGAM'

Packages suggested but not available for checking:
  'R.rsp', 'CascadeData', 'knitr'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'htmltools', 'magrittr', 'rlang'

Packages suggested but not available for checking:
  'rmarkdown', 'shiny', 'testthat'

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

Packages suggested but not available for checking:
  'dse', 'expsmooth', 'fBasics', 'FitARMA', 'fGarch', 'forecast',
  'polynom', 'timeSeries', 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R2HTML', 'fitdistrplus', 'moments', 'copula', 'scatterplot3d'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'eha', 'gbm', 'glmnet', 'knitr', 'rmarkdown', 'colorspace', 'visreg',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'dplyr', 'haven', 'labelled', 'glue', 'magrittr', 'tidyr',
  'tibble', 'janitor', 'survey', 'srvyr', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'testthat', 'broom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'tibble', 'tidyr', 'purrr', 'crayon', 'R6',
  'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'beepr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bipartite', 'reshape2', 'magrittr', 'vegan', 'purrr', 'dplyr',
  'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pROC'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'naturalsort', 'nloptr', 'RSpectra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'ggplot2', 'reshape', 'FNN', 'plyr', 'zoo', 'data.table'

Packages suggested but not available for checking:
  'doParallel', 'randomForest', 'lubridate', 'raster', 'sp', 'knitr',
  'mapview', 'rmarkdown', 'sf', 'scales', 'latticeExtra',
  'virtualspecies', 'gridExtra', 'viridis', 'rgeos', 'stars', 'scam'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'caret', 'progress', 'randomForest', 'tidyr', 'dplyr',
  'data.table', 'assertthat'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pacman', 'testthat', 'magrittr', 'igraph'

VignetteBuilder package required for checking but not installed: 'knitr'

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:
  'DBI', 'knitr', 'pkgdown', 'rmarkdown', 'roxygen2', 'tinytest'

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

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

Packages suggested but not available for checking:
  'testthat', 'beepr', 'crayon', 'covr', 'knitr', 'rmarkdown',
  'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

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', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rms', 'qvcalc', 'glmmML', 'pscl', 'VGAM', 'gee', 'mlogit', 'Ecdat',
  'geepack', 'party', 'ordinal', 'lme4', 'vcdExtra', 'glmnet',
  'mboost', 'e1071', 'flexmix', 'lpSolve', 'GAMBoost', 'penalized'
Packages required but not available: 'Rglpk', 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'sparsepca', 'data.table'

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'esaBcv', 'ruv', 'sva', 'corpcor', 'leapp'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/cate-vignette.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
MDR.high.forward1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for
  'complete.cases'
MDR.sing.mod1: no visible global function definition for 'lm'
MDR.sing.mod1: no visible global function definition for 'aov'
MDR.sing.mod1: no visible global function definition for 'anova'
MDR.stage.forward1: no visible global function definition for 'combn'
MDR.stage.forward1: no visible global function definition for
  'complete.cases'
MDR.stage.forward1: no visible global function definition for 'lm'
MDR.stage.forward1: no visible global function definition for 'resid'
MDR.stage.forward1: no visible global function definition for 'pf'
MDR_forward1: no visible global function definition for
  'complete.cases'
MDR_forward1: no visible global function definition for 'lm'
MDR_forward1: no visible global function definition for 'aov'
low.anova: no visible global function definition for 'complete.cases'
low.anova: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'combn'
sing.mod1: no visible global function definition for 'complete.cases'
sing.mod1: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available:
  'epitools', 'DescTools', 'cli', 'magrittr', 'Hmisc', 'broom', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'ape', 'e1071', 'rasterVis', 'hypervolume', 'FD', 'geometry',
  'vegan'

Packages suggested but not available for checking:
  'spacodiR', 'entropart', 'fBasics', 'picante', 'mice', 'knitr'

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

Packages suggested but not available for checking: 'irtoys', 'ltm', 'catR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'png', 'rtf', 'season', 'magic', 'signal', 'assertr', 'CombMSC',
  'Hmisc'

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

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', 'tidyverse', 'dplyr', 'lubridate', 'magrittr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'viridis', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

> ### Name: cnSetProb-method
> ### Title: Set Probability from Data
> ### Aliases: cnSetProb cnSetProb,catNetwork-method
> ###   cnSetProb,catSampleNetwork-method
> ### Keywords: methods graphs
> 
> ### ** Examples
> 
>   library(catnet)
>   cnet <- cnRandomCatnet(numnodes=10, maxParents=3, numCategories=3)
Package required but not available: 'bitops'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable 'var'
mi.inference: no visible global function definition for 'qt'
mi.inference: no visible global function definition for 'pt'
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'emmeans'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'testthat'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mlogit'
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for 'xtabs'
mob.eqmain: no visible global function definition for 'model.matrix'
mob.qi: no visible global function definition for 'C'
mob.qi: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'C'
mob.rc1: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'model.matrix'
mob.symint: no visible global function definition for 'model.matrix'
print.ctab: no visible global function definition for 'ftable'
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
Packages unavailable to check Rd xrefs: 'gmodels', 'mlogit'
Packages required but not available:
  'ltm', 'jsonlite', 'plyr', 'Rcpp', 'RcppParallel', 'BH',
  'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking:
  'catIrt', 'catR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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', 'purrr', 'rlang', 'tibble', 'tidyselect', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'knitr', 'lintr', 'nycflights13', 'ranger', 'rmarkdown',
  'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DiagrammeR', 'dplyr', 'magrittr', 'ggplot2', 'rlang', 'greta',
  'purrr', 'tidyr', 'igraph', 'stringr', 'cowplot', 'coda', 'forcats',
  'htmlwidgets', 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'inline', 'doParallel', 'foreach', 'data.table', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', 'tidyverse', 'ggalt', 'cobalt',
  'ggsci', 'modEvA', 'naniar', 'DT', 'Hmisc', 'hrbrthemes',
  'summarytools', 'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'BayesTree', 'dplyr', 'Hmisc', 'knitr', 'reshape2', 'rmarkdown',
  'sas7bdat', 'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Using_causaldrf.Rnw'
(Is a VignetteBuilder field missing?)

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

Packages suggested but not available for checking: 'R.rsp', 'XML'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fda', 'cvTools', 'quadprog', 'randomForest', 'deSolve', 'pspline',
  'glmnet', 'sundialr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'KFAS', 'CholWishart', 'forecast', 'MixMatrix'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'Rcpp', 'dagitty', 'gtools', 'randomizr', 'rlang', 'rstan',
  'rstantools', 'stringr', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr', 'DeclareDesign', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/causalsens.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/causalsens.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available:
  'ranger', 'mvtnorm', 'np', 'LARF', 'hdm', 'SuperLearner', 'glmnet',
  'xgboost', 'e1071', 'fastDummies'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'spc', 'sitmo', 'BH'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'metap', 'magrittr', 'dplyr', 'tibble', 'stringr', 'ggplot2',
  'tidyr', 'glue', 'pheatmap', 'readr', 'R.utils', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

> ### Name: bcr
> ### Title: Benefit Cost Ratio
> ### Aliases: bcr
> 
> ### ** Examples
> 
> tb = data.frame(cost=c(2500, 28000,15800.50), benefit=c(2600.95,30600,16200.50),
+ rate = c(4,4,4.2), no.of.years=c(1,1,1))
> bc = bcr(tb)
Error in assign("Discounted_cost", c(), envir = .BaseNamespaceEnv) : 
  cannot add binding of 'Discounted_cost' to the base environment
Calls: bcr -> assign
Execution halted
Package required but not available: 'proxy'

Packages suggested but not available for checking: 'gclus', 'colorspace'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'prettydoc', 'foreach', 'SuperLearner', 'doParallel'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'FNN', 'e1071', 'missForest', 'knockoff',
  'caret', 'smotefamily', 'xgboost', 'bartMachine', 'glmnet',
  'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Formula', 'Rcpp', 'rstan', 'rstantools', 'BH', 'RcppEigen',
  'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Packages required but not available: 'whisker', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'shiny', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'dplyr', 'raster', 'rgdal', 'rgeos', 'geosphere', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pcaPP', 'robustbase', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'mvtnorm'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/ccaPP-intro.Rnw'
(Is a VignetteBuilder field missing?)

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.
Packages required but not available: 'mpath', 'xgboost'

Packages suggested but not available for checking: 'R.rsp', 'DiagrammeR'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'proxy', 'deldir', 'FNN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
VD: no visible binding for global variable 'var'
stratcc : <anonymous>: no visible global function definition for
  'hclust'
stratcc : <anonymous>: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'RUnit', 'numDeriv'

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

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

Packages suggested but not available for checking:
  'testthat', 'graph', 'igraph'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'IDetect', 'hdbinseg', 'GeneNet', 'gdata'

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', 'httr', 'jsonlite', 'keyring', 'lubridate', 'purrr',
  'tibble', 'rlang'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'knitr', 'msm', 'forcats', 'rlang',
  'data.table', 'Rdpack'

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

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
p.Roy: no visible global function definition for 'pf'
p.asym: no visible global function definition for 'pf'
p.perm: no visible global function definition for 'cancor'
plt.asym: no visible global function definition for 'qf'
plt.asym: no visible global function definition for 'df'
plt.asym: no visible global function definition for 'abline'
plt.perm: no visible global function definition for 'hist'
plt.perm: no visible global function definition for 'mtext'
plt.perm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cancor df hist mtext pf qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'cds', 'colorspace', 'dplyr', 'limSolve', 'lsbclust', 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'testthat', 'Rcpp', 'expint', 'pracma'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R2jags', 'rjags', 'psych', 'mvtnorm', 'polycor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'Formula', 'formula.tools', 'ddpcr', 'RcppArmadillo',
  'RcppProgress'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'DBI', 'RSQLite', 'knitr', 'rmarkdown', 'yaml', 'tinytest'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GDINA', 'ggplot2', 'cowplot', 'foreach', 'doSNOW', 'NPCD'

Package suggested but not available for checking: 'CDM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'progress', 'dplyr', 'jsonlite', 'tibble', 'sf', 'xml2',
  'purrr', 'readr', 'MMWRweek', 'units'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'glue', 'stringr', 'tibble', 'dplyr', 'readr', 'rlang',
  'lubridate'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'polycor', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds', 'ROI', 'sirt', 'sfsmisc'

Packages which this enhances but not available for checking:
  'dina', 'GDINA', 'mirt', 'rrum', 'TAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tframe', 'tfplot'
Package unavailable to check Rd xrefs: 'tframe'
Running examples in 'CDNmoney-Ex.R' failed
The error most likely occurred in:

> ### Name: CanadianCreditData
> ### Title: Canadian Credit Aggregates
> ### Aliases: CanadianCreditData CanadianCreditData.asof.6Mar2009
> ###   CanadianCreditData.asof.5Jun2007 CanadianCreditData.asof.3Mar2006
> ###   CanadianCreditData.asof.28Jan2005 TotalCredit ConsumerCredit
> ###   ResidentialMortgage ShortTermBusinessCredit OtherBusinessCredit
> ### Keywords: datasets
> 
> ### ** Examples
> 
>  require("tframe")
Loading required package: tframe
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'tframe'
>  require("tfplot")
Loading required package: tfplot
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'tfplot'
>  data("CanadianCreditData", package="CDNmoney")
> 
>  tfplot(TotalCredit, ConsumerCredit, ResidentialMortgage,
+     ShortTermBusinessCredit, OtherBusinessCredit) 
Error in tfplot(TotalCredit, ConsumerCredit, ResidentialMortgage, ShortTermBusinessCredit,  : 
  could not find function "tfplot"
Execution halted
Running 'aggtst01.R'
Running the tests in 'tests/aggtst01.R' failed.
Last 13 lines of output:
  > require("tfplot")
  Loading required package: tfplot
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'tfplot'
  > 
  > data("CanadianMoneyData.asof.26Aug2002", package="CDNmoney")
  > 
  > if(!require("tframe")) stop("This test requires the tframe package.")
  Loading required package: tframe
  Error: This test requires the tframe package.
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'tframe'
  Execution halted
Packages required but not available:
  'minpack.lm', '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:
  'data.table', 'plotly', 'freqparcoord', 'partools'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'foreach', 'doParallel', 'dirmult', 'RcppThread',
  'iterators', 'qlcMatrix', 'gplots', 'clue', 'Biobase', 'Seurat',
  'ggplot2', 'magrittr', 'dplyr', 'rlang', 'matrixStats', 'ggpubr',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'limSolve', 'clue', 'colorspace', 'copula'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fastmatch', 'jsonlite', 'mongolite', 'readr', 'shiny', 'udpipe'

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

Packages suggested but not available for checking: 'tinytest', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DEoptim', 'quadprog', 'ParamHelpers', 'fastmatch'

Package suggested but not available for checking: 'nloptr'

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

Package suggested but not available for checking: 'testthat'

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

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

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

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'pracma', 'scatterplot3d', 'fractaldim', 'testthat', 'wordspace',
  'knitr', 'rmarkdown', 'uwot', 'dendextend', 'ggplot2', 'ggbeeswarm',
  'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'scales', 'ggplot2', 'matrixStats', 'gridExtra',
  'robustbase', 'rrcov', 'svd', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'robustHD', 'ellipse', 'markdown', 'rospca', 'GSE'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clusteval', 'doParallel', 'rootSolve', 'foreach', 'mclust',
  'mvtnorm'

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

Package suggested but not available for checking: 'Amelia'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'mvtnorm', 'glmnet', 'cvTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'doSNOW', 'foreach', 'magrittr', 'pbapply', 'Rcpp', 'snow',
  'sp'

Packages suggested but not available for checking:
  'knitr', 'maps', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'icenReg', 'condSURV', 'RcppEigen'

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

Package suggested but not available for checking: 'mixsmsn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cenNID: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Packages required but not available:
  'DBI', 'duckdb', 'httr', 'tibble', 'purrr', 'cli', 'crayon',
  'rstudioapi'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'dplyr', 'dbplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for 'dnorm'
MomNIT: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
em.cens: no visible global function definition for 'lm'
em.cens: no visible global function definition for 'coefficients'
em.cens : ft: no visible global function definition for 'dt'
em.cens : ft: no visible global function definition for 'pt'
em.cens: no visible global function definition for 'optimize'
em.cens: no visible global function definition for 'dnorm'
em.cens: no visible global function definition for 'pnorm'
em.cens: no visible global function definition for 'sd'
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
Packages required but not available:
  'maxLik', 'glmmML', 'sandwich', 'miscTools', 'plm'

Packages suggested but not available for checking: 'AER', 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geoR', 'mvtnorm', 'optimx', 'tmvtnorm', 'msm', 'psych', 'numDeriv',
  'raster', 'moments', 'tlrmvnmvt'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'ggrepel', 'magrittr', 'scales',
  'testthat', 'png'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'sf', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'stringi', 'purrr'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: 'expm', 'linkcomm'

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: 'pracma'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gravity'
Note: found 104 marked UTF-8 strings
Packages required but not available: 'astsa', 'multitaper'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'vegan'
Packages required but not available:
  'httr', 'tibble', 'magrittr', 'dplyr', 'purrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'slippymath', 'curl', 'dplyr', 'fs', 'glue', 'rappdirs', 'tibble',
  'purrr', 'magrittr', 'rlang', 'sp', 'raster', 'spex', 'jpeg', 'png',
  'reproj'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rgdal', 'spelling'

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

Packages suggested but not available for checking:
  'rrcov', 'robust', 'mvtnorm', 'alr3'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
select_lambda: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tidyr', 'RColorBrewer'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'ggplot2', 'gower', 'DALEX', 'knitr'

Packages suggested but not available for checking:
  'randomForest', 'ggiraph', 'e1071', 'testthat'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'abind', 'doParallel', 'foreach', 'RcppArmadillo',
  'RcppProgress'

Packages suggested but not available for checking:
  'BSGW', 'BayesMixSurv', 'Hmisc', 'randomForestSRC', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Packages required but not available:
  'rgdal', 'raster', 'foreach', 'data.table', 'geosphere', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'magrittr', '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: 'coneproj', 'svDialogs', 'lme4'

Package suggested but not available for checking: 'SemiPar'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R.oo', 'R.methodsS3', 'httr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'ggplot2', 'reshape2', 'plyr', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'tkrplot', 'GLAD'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'nleqslv', 'data.table', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'pracma', 'zoo', 'pastecs', 'readxl',
  'readr', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'tidyverse', 'ggplot2', 'hms', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BayesFactor', 'DescTools', 'dplyr', 'forcats', 'ggmosaic',
  'ggplot2', 'ggrepel', 'paletteer', 'partykit', 'purrr', 'rlang',
  'scales', 'sjstats', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'BSDA', 'ggthemes', 'hrbrthemes', 'janitor', 'knitr', 'lsr',
  'magrittr', 'productplots', 'pwr', 'rmarkdown', 'stringi', 'tibble',
  'testthat', 'tidyselect'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > # 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', 'VGAM', 'multcomp', 'rms'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'actuar', 'tweedie', 'systemfit', 'statmod', 'cplm', 'ggplot2'

Packages suggested but not available for checking:
  'RUnit', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'sandwich', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rdpack', 'L1pack', 'glmnet'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'zoo', 'tbart', 'Rdpack', 'ggplot2', 'reshape2', 'assertive'

Package suggested but not available for checking: 'gridExtra'

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

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

Package suggested but not available for checking: 'testthat'

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

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

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'available', 'devtools', 'git2r'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'pbdMPI', 'tuneR'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'gridExtra', 'sphereplot', 'plot3D', 'rgl',
  'RColorBrewer', 'colorRamps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Hartree2Joule: no visible binding for global variable
  'universalConstants'
Hertz2Joule: no visible binding for global variable
  'universalConstants'
Joule2Hartree: no visible binding for global variable
  'universalConstants'
Joule2Hertz: no visible binding for global variable
  'universalConstants'
Joule2Kelvin: no visible binding for global variable
  'universalConstants'
Joule2centimeterMinusOne: no visible binding for global variable
  'universalConstants'
Joule2electronVolt: no visible binding for global variable
  'universalConstants'
Joule2kiloCaloriePerMole: no visible binding for global variable
  'universalConstants'
Joule2kiloJoulePerMole: no visible binding for global variable
  'universalConstants'
KMC: no visible global function definition for 'runif'
Kelvin2Joule: no visible binding for global variable
  'universalConstants'
LandauZener: no visible binding for global variable
  'universalConstants'
LandauZenerProbability: no visible binding for global variable
  'universalConstants'
Marcus: no visible binding for global variable 'universalConstants'
MarcusLevichJortner: no visible binding for global variable
  'universalConstants'
centimeterMinusOne2Joule: no visible binding for global variable
  'universalConstants'
electronVolt2Joule: no visible binding for global variable
  'universalConstants'
kiloCaloriePerMole2Joule: no visible binding for global variable
  'universalConstants'
kiloJoulePerMole2Joule: no visible binding for global variable
  'universalConstants'
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'R6', 'tibble', 'whisker'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'iptools', 'stringi'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'textreadr', 'ngram', 'purrr', 'R.utils'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'devtools', 'shiny', 'DT',
  'ggplot2', 'tidygraph', 'ggraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'git2r', 'fs', 'crayon', 'cli', 'purrr', 'rappdirs',
  'stringr', 'rstudioapi'

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

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

Packages suggested but not available for checking:
  'knitr', 'cubature', 'plot3D'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/chebpol.Rnw'
   'inst/doc/chebusage.Rnw'
   'inst/doc/stalker.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'testthat'
Malformed Description field: should contain one or more complete sentences.
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 required but not available: 'knitr', 'markdown'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'R6', 'fastmatch', 'data.table', 'devtools', 'ggplot2', 'knitr',
  'magrittr', 'microbenchmark', 'rmarkdown', 'testthat', 'tinytest',
  'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'darts', 'mockery', 'cli'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'knitr'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(cli)
  Error in library(cli) : there is no package called 'cli'
  Execution halted
Package required but not available: 'err'

Packages suggested but not available for checking:
  'assertthat', 'checkmate', 'covr', 'magrittr', 'hms', 'dplyr',
  'units', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'kableExtra', 'knitr', 'magrittr', 'purrr',
  'rlang', 'stringr', 'tibble', 'tidyr', 'tidyselect'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'testthat', 'investr', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'fingerprint', 'rcdk', 'MSQC', 'e1071', 'elasticnet', 'lars', 'pROC',
  'randomForest', 'tree', 'pls', 'caret'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'pcaPP', 'robustbase', 'som', 'lars', 'pls', 'mclust'

Package suggested but not available for checking: 'gclus'

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

Packages suggested but not available for checking:
  'knitr', 'tinytest', 'irlba', 'ThreeWay', 'multiway', 'matrixStats',
  'R.utils', 'mlrMBO', 'ParamHelpers', 'smoof', 'mlr', 'lhs',
  'RcppRoll', 'rmarkdown', 'pinp', 'robustbase', 'bookdown', 'CMLS'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'IDPmisc', 'knitr', 'js', 'NbClust', 'baseline', 'mclust', 'pls',
  'clusterCrit', 'R.utils', 'RColorBrewer', 'seriation', 'robustbase',
  'pcaPP', 'jsonlite', 'gsubfn', 'signal', 'rgl', 'speaq', 'tinytest',
  'elasticnet', 'irlba', 'amap', 'rmarkdown', 'bookdown',
  'chemometrics', 'hyperSpec'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'ChemoSpec', 'ChemoSpec2D', 'tinytest', 'robustbase', 'RColorBrewer',
  'amap', 'irlba', 'ThreeWay', 'multiway', 'roxut'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
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
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: 'bitops', 'lpSolve', 'hommel'

Package suggested but not available for checking: 'multtest'

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'png', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gamlss.tr', 'gamlss', 'data.table', 'foreach', 'doParallel',
  'iterators', 'bedr', 'knitr', 'rmarkdown'

Packages suggested but not available for checking:
  'testthat', 'GenomicInteractions', 'GenomicRanges', 'Gviz',
  'countreg'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'bigstatsr', 'RcppParallel', 'mvnfast', 'zipfR', 'pracma',
  'nloptr', 'foreach', 'doRNG', 'doParallel', 'Rdpack',
  'RcppArmadillo', 'rmio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
Packages required but not available:
  'DBI', 'dbplyr', 'dplyr', 'jsonlite', 'magrittr', 'purrr', 'RMySQL'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'curl'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gamlss', 'gamlss.dist', 'dplyr', 'magrittr', 'tidyr', 'tibble',
  'reshape2', 'purrr', 'purrrlyr', 'VGAM'

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', 'magrittr', 'stringr', 'rlang'

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

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'chillR', 'dplyr', 'lubridate', 'ggplot2'
Package unavailable to check Rd xrefs: 'chillR'
Packages required but not available:
  'pls', 'dplyr', 'rlang', 'Kendall', 'fields', 'sp', 'readxl', 'XML',
  'httr', 'jsonlite', 'RMAWGEN', 'RCurl', 'R.utils', 'raster',
  'ggplot2', 'assertthat', 'reshape2', 'plyr', 'Rcpp', 'GenSA'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jiebaR', 'NLP', 'tm', 'stringi', 'slam', 'purrr'

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

Packages suggested but not available for checking: 'babynames', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lmtest', 'outliers', 'ptw', 'quantreg', 'Rfit', 'robustbase',
  'shiny', 'signal'

Packages suggested but not available for checking:
  'drc', 'knitr', 'markdown', 'qpcR', 'RDML', 'rmarkdown', 'spelling',
  'testthat', 'tinytex', 'xtable'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

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

Packages suggested but not available for checking:
  'knitr', 'markdown', 'rmarkdown', 'testthat', 'vcr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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: 'lifecycle', 'rlang'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'mclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', '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: 'kyotil', 'lme4'

Packages suggested but not available for checking:
  'R.rsp', 'RUnit', 'mvtnorm'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tufte'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: '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: 'AlgDesign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'bayesm'
File
  LICENSE
is not mentioned in the DESCRIPTION file.
choicemodelr : drawDelta: no visible global function definition for
  'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'runif'
choicemodelr : rmultireg: no visible global function definition for
  'rnorm'
choicemodelr : rwishart: no visible global function definition for
  'rchisq'
choicemodelr : rwishart: no visible global function definition for
  'rnorm'
choicemodelr : fsh: no visible global function definition for
  'flush.console'
choicemodelr: no visible global function definition for 'matplot'
choicemodelr: no visible global function definition for 'write.table'
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deldir', 'ggplot2', 'HistData', 'igraph', 'pracma', 'RColorBrewer',
  'sp', 'threejs', 'TSP', 'viridisLite'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'coin'
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for 'var'
Qh.times.dhyper: no visible global function definition for 'pnorm'
Qh.times.dhyper: no visible global function definition for 'dhyper'
TDiM: no visible global function definition for 'sd'
choplump.default: no visible global function definition for
  'flush.console'
choplump.formula: no visible global function definition for 'terms'
cm.compact: no visible global function definition for 'dhyper'
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Errors in running code in vignettes:
when running code in 'choplumpValidation.Rnw'
  ...
calculating exact test...
requires  62  evaluations of test statistic
  p.lower   p.upper  p.2sided 
0.6349206 0.3809524 0.7619048 

> library(coin)

  When sourcing 'choplumpValidation.R':
Error: there is no package called 'coin'
Execution halted

  'choplumpValidation.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'choplumpValidation.Rnw' using Sweave

Error: processing vignette 'choplumpValidation.Rnw' failed with diagnostics:
 chunk 6 
Error in library(coin) : there is no package called 'coin'

--- failed re-building 'choplumpValidation.Rnw'

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

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

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'
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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggplot2'
Packages required but not available:
  'acs', 'Hmisc', 'stringr', 'ggplot2', 'dplyr', 'R6', 'WDI', 'ggmap',
  'RgoogleMaps', 'tigris', 'gridExtra', 'xml2', 'rvest', 'tidyr',
  'tidycensus'

Packages suggested but not available for checking:
  'testthat', 'choroplethrMaps', 'choroplethrAdmin1'

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

Packages suggested but not available for checking: 'graph', 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'dplyr', 'xml2', 'rvest', 'magrittr', 'purrr', 'forcats',
  'rlang'

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

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

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

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: 'htmltools', 'htmlwidgets'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Packages required but not available:
  'rlang', 'magrittr', 'data.table', 'DT', 'dygraphs', 'ggplot2',
  'glue', 'knitr', 'plotly', 'prettydoc', 'purrr', 'readr',
  'rmarkdown', 'rmdformats', 'scales', 'skimr', 'viridis', 'zoo'

Packages suggested but not available for checking:
  'bookdown', 'devtools', 'flexdashboard', 'pagedown', 'rolldown',
  'rticles', 'tufte', 'xaringan'

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

Packages suggested but not available for checking:
  'jpeg', 'knitr', 'ncdf4', 'rgdal', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'scales', 'ggplot2'

Package which this enhances but not available for checking: 'zoo'
Packages unavailable to check Rd xrefs: 'ggplot2', 'zoo'
Package required but not available: 'scatterplot3d'

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

Packages suggested but not available for checking:
  'testthat', 'RSQLite', 'dbplyr'

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

Packages suggested but not available for checking:
  'spelling', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'R6', 'shiny', 'assertthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'lavaan', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'lavaan'
'LazyData' is specified without a 'data' directory
Running examples in 'CIEE-Ex.R' failed
The error most likely occurred in:

> ### Name: ciee
> ### Title: CIEE: Causal inference based on estimating equations
> ### Aliases: ciee ciee_loop
> 
> ### ** Examples
> 
> 
> # Generate data under the GLM setting with default values
> maf <- 0.2
> n <- 100
> dat <- generate_data(n = n, maf = maf)
> datX <- data.frame(X = dat$X)
> names(datX)[1] <- "X1"
> # Add 9 more exposure variables names X2, ..., X10 to X
> for (i in 2:10){
+   X <- stats::rbinom(n, size = 2, prob = maf)
+   datX$X <- X
+   names(datX)[i] <- paste("X", i, sep="")
+ }
> 
> # Perform analysis of one exposure variable using all four methods
> ciee(Y = dat$Y, X = datX$X1, K = dat$K, L = dat$L)
Error: Pkg needed for this function to work. Please install it.
Execution halted
Package required but not available: 'lubridate'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'oro.nifti', 'gifti', 'R.utils'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'rgl', 'matrixStats'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'gifti', 'oro.nifti', 'RNifti', 'RColorBrewer', 'rgl',
  'viridisLite', 'xml2'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'ggpubr', 'htmlwidgets', 'knitr', 'rmarkdown',
  'papayar', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'glue', 'stringr', 'dplyr', 'tidyr', 'jsonlite', 'purrr',
  'rlang'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BART', 'twang', 'arm', 'dplyr', 'Matching', 'magrittr', 'car',
  'WeightIt', 'SuperLearner', 'tmle', 'tidyr', 'gam', 'dbarts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ChIPseeker', 'DESeq2', 'dplyr', 'edgeR', 'fgsea', 'GenomicRanges',
  'ggplot2', 'ggrepel', 'limma', 'pheatmap', 'preprocessCore',
  'RColorBrewer', 'sva', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'writexl'

Packages suggested but not available for checking:
  'biomaRt', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'network', 'sna', 'centiserve', 'FactoMineR', 'factoextra',
  'GGally', 'pheatmap', 'corrplot', 'dendextend', 'viridis', 'ggplot2',
  'Rtsne', 'qdapTools', 'plyr', 'circlize', 'intergraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cin: no visible global function definition for 'pnorm'
gammaHRF: no visible global function definition for 'dgamma'
intertest: no visible global function definition for 'pnorm'
truncSum: no visible global function definition for 'spline'
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'multcomp'

Packages suggested but not available for checking:
  'BSDA', 'fmsb', 'userfriendlyscience'

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', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'shiny', 'ggplot2', 'reshape2', 'coda', 'BH', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'clipr', 'covr', 'gert', 'gh', 'knitr', 'openssl', 'purrr',
  'rmarkdown', 'testthat', 'usethis', 'vcr', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

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

Packages suggested but not available for checking:
  'knitr', 'dendextend', 'ComplexHeatmap', 'gridBase', 'png',
  'markdown', 'bezier'

VignetteBuilder package required for checking but not installed: 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'circular', 'RInside', 'coda', 'ggplot2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'foreach', 'iterators', 'doParallel', 'gridExtra'

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

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

Packages suggested but not available for checking:
  'plotly', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'ggforce', 'ggplot2', 'glue', 'htmlTable',
  'magrittr', 'purrr', 'Rcpp', 'rlang', 'tibble', 'tidyr',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'knitr', 'rmarkdown', 'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'far', 'gdata', 'glmnet', 'rARPACK'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'agop', 'RSQLite', 'RGtk2', 'hash', 'stringi', 'DBI'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cit.assignBcmst: no visible binding for global variable 'citbcmst'
cit.assignBcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignBcmst: no visible global function definition for 'prcomp'
cit.assignBcmst: no visible global function definition for 'par'
cit.assignBcmst: no visible global function definition for 'lines'
cit.assignBcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable 'citccmst'
cit.assignCcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignCcmst : median.na: no visible global function definition for
  'median'
cit.assignCcmst: no visible global function definition for 'prcomp'
cit.assignCcmst: no visible global function definition for 'par'
cit.assignCcmst: no visible global function definition for 'lines'
cit.assignCcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
Packages required but not available:
  'crul', 'data.table', 'fauxpas', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'vcr', 'webmockr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arm', 'dplyr', 'lme4'

Packages suggested but not available for checking:
  'here', 'ggplot2', 'knitr', 'rmarkdown', 'SPREDA'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for 'read.table'
CityPlot: no visible global function definition for 'tail'
CityPlot: no visible global function definition for 'pdf'
CityPlot: no visible global function definition for 'split.screen'
CityPlot: no visible global function definition for 'screen'
CityPlot: no visible global function definition for 'par'
CityPlot: no visible global function definition for 'rect'
CityPlot: no visible global function definition for 'text'
CityPlot: no visible global function definition for 'lines'
CityPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
Packages required but not available:
  'dataRetrieval', 'dplyr', 'EcoHydRology', 'geoknife', 'lubridate',
  'reshape2', 'tgp', 'xts', 'zoo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'caret', 'gbm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'functional', 'nloptr', 'pracma', 'PreciseSums', 'statmod'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nloptr', 'statmod', 'functional', 'pracma'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'future', 'httr', 'jsonlite', 'memoise'

Packages suggested but not available for checking:
  'feather', 'ggplot2', 'knitr', 'rmarkdown', 'roxygen2', 'mockery',
  'R.utils', 'rstudioapi', 'testthat', 'yaml'

VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sandwich', 'lmtest', 'ggplot2', 'survey', 'DT', 'shiny', 'shinyjs',
  'shinyBS'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'crul', 'jsonlite', 'dplyr', 'dbplyr', 'magrittr'

Packages suggested but not available for checking:
  'sf', 'readxl', 'testthat', 'xml2', 'lazyeval'

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

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'phytools', 'strap', 'clipr', 'geoscale'

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'R.cache', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'fGarch', 'FRAPO'
Packages unavailable to check Rd xrefs: 'FRAPO', 'fGarch'
Packages required but not available: 'curl', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'oompaBase', 'mclust', 'oompaData', 'Biobase'

Package suggested but not available for checking: 'xtable'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'data.table', 'Rcpp', 'ROCR', 'caret', 'gridExtra', 'png'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: 'e1071', 'rggobi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking: 'testthat', 'cld2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
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
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'R.rsp'
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Packages suggested but not available for checking: 'rmarkdown', 'testthat'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'rasciidoc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH'

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', 'sp', 'raster', 'reshape2', 'plyr', 'scales'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'selectr', 'withr', 'xml2'

Packages suggested but not available for checking:
  'callr', 'covr', 'rstudioapi', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'beeswarm', 'flextable', 'lme4', 'lmerTest', 'officer', 'stringdist',
  'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'reshape2', 'plyr', 'Rsolnp', 'arules', 'linprog',
  'ggplot2', 'ClickClust', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'RColorBrewer', 'reshape2', 'rvest'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package suggested but not available for checking: 'fracdiff'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'lubridate', 'stringr', 'scales',
  'ggplot2', 'ggpubr', 'ggthemes', 'gtable', 'gganimate',
  'RColorBrewer', 'jpeg', 'httr', 'jsonlite', 'climatol', 'rlang',
  'magrittr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'learnr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'httr', 'curl'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking: 'knitr', 'rangeBuilder'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maps', 'mapdata'

Packages suggested but not available for checking:
  'fields', 'gstat', 'ncdf4', 'raster', 'RODBC', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'PCICt', 'Rcpp'

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpSolve'

Packages suggested but not available for checking: 'lorec', 'scio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'extRemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SPEI', 'chron', 'weathermetrics'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'reshape', 'numDeriv', 'RcppRoll'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'shiny', 'waiter', 'foreach', 'ggplot2', 'DoseFinding',
  'doParallel', 'magrittr', 'purrr', 'tibble', 'dplyr', 'tidyr', 'glue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'ggplot2', 'cowplot', 'nloptr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'signal'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'testit', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'reticulate', 'data.table', 'assertthat', 'rappdirs', 'magrittr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
gxe.cc: no visible global function definition for 'qnorm'
gxe.coh: no visible global function definition for 'qnorm'
utility.cc: no visible global function definition for 'qnorm'
utility.coh: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Skipping vignette re-building
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'LazyData' is specified without a 'data' directory
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:
  'colorspace', 'igraph', 'magrittr', 'Polychrome', 'qgraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glue'

Packages suggested but not available for checking:
  'callr', 'covr', 'htmlwidgets', 'knitr', 'mockery', 'ps',
  'rmarkdown', 'rstudioapi', 'prettycode', 'testthat', 'withr'

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
Packages required but not available:
  'shiny', 'lme4', 'isotone', 'stringr', 'prettyR', 'openxlsx'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ellipsis', 'rlang', 'tzdb', 'vctrs', 'cpp11'

Packages suggested but not available for checking:
  'covr', 'knitr', 'magrittr', 'pillar', 'rmarkdown', 'testthat',
  'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lassoshooting', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'combinat', 'gtools', 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sets', 'ggplot2', 'ggrepel', 'arules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pbivnorm', 'rootSolve', 'doParallel', 'foreach', 'tmvmixnorm',
  'ttutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tfruns', 'config', 'jsonlite', 'packrat', 'processx', 'rprojroot',
  'rstudioapi', 'withr', 'yaml'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'lubridate', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
socp: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Package required but not available: 'sandwich'

Packages suggested but not available for checking:
  'Formula', 'knitr', 'carData', 'geepack', 'metafor', 'robumeta',
  'mlmRev', 'AER', 'plm', 'lme4', 'zoo', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
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Packages which this enhances but not available for checking:
  'RWeka', 'ape', 'cba', 'cclust', 'flexclust', 'flexmix', 'kernlab',
  'mclust', 'movMF', 'modeltools'
Unavailable namespace imported from by a ':::' call: 'relations'
  See the note in ?`:::` about the use of this operator.
Packages unavailable to check Rd xrefs: 'mlbench', 'ape', 'e1071', 'fpc', 'cclust', 'lpSolve'
Errors in running code in vignettes:
when running code in 'clue.Rnw'
  ...

> set.seed(1)

> m1 <- cl_consensus(GVME, method = "GV1", control = list(k = 3, 
+     verbose = TRUE))
Iteration: 0 *** value: 7.26349

  When sourcing 'clue.R':
Error: there is no package called 'quadprog'
Execution halted

  'clue.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'clue.Rnw' using Sweave
Iteration: 0 *** value: 7.26349

Error: processing vignette 'clue.Rnw' failed with diagnostics:
 chunk 14 
Error in loadNamespace(x) : there is no package called 'quadprog'

--- failed re-building 'clue.Rnw'

SUMMARY: processing the following file failed:
  'clue.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'NbClust', 'amap', 'tableone', 'data.table',
  'rlang'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'VennDiagram', 'scales', 'reshape2', 'ggplot2', 'rlang'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'fastcluster', 'rlang', 'igraph', 'magrittr',
  'Rcpp'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

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: 'FactoMineR'

Package suggested but not available for checking: 'ClustVarLV'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'ggplot2', 'ggfortify', 'doRNG', 'Gmedian',
  'npregfast', 'RColorBrewer'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'caret', 'ORCME', 'ORIClust', 'multcomp',
  'IsoGene', 'DoseFinding', 'pheatmap', 'shiny', 'readr', 'DT',
  'MCPMod', 'RColorBrewer'

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.
Package required but not available: 'diptest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'RUnit', 'rbenchmark'
Packages required but not available:
  'Formula', 'cubature', 'lme4', 'numDeriv', 'rootSolve'

Packages suggested but not available for checking:
  'testthat', 'rprojroot', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'seriation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
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  'doParallel', 'dplyr', 'foreach', 'future', 'gama', 'ggplot2', 'gmp',
  'pracma', 'pvclust', 'shiny', 'sqldf', 'xtable'

Packages suggested but not available for checking:
  'DT', 'kableExtra', 'knitr', 'rmarkdown', 'shinyalert', 'shinyFiles',
  'shinyjs', 'shinythemes', 'shinyWidgets', 'tidyverse',
  'shinycssloaders'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'GSEABase', 'GSVA', 'magrittr', 'rlang', 'singscore',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'knitr', 'prettydoc', 'rmarkdown', 'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'narray', 'progress', 'purrr', 'R6', 'Rcpp'

Packages suggested but not available for checking:
  'callr', 'devtools', 'dplyr', 'foreach', 'iterators', 'knitr',
  'rmarkdown', 'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'plyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'mclust', 'gplots', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

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', 'clValid', 'data.tree', 'dendextend', 'jsonlite', 'mclust',
  'RCurl', 'reshape', 'reshape2', 'stringr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'progress', 'dplyr', 'tidyr', 'R.utils', 'car', 'lmerTest',
  'foreach', 'shiny', 'mathjaxr'

Packages suggested but not available for checking:
  'geepack', 'nloptr', 'optimx', 'doParallel', 'shinyBS', 'tidyverse',
  'DT', 'stringr', 'CRTSize', 'data.table', 'testthat', 'knitr',
  'rmarkdown', 'shinycssloaders'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'mvoutlier', 'fpc', 'ellipse', 'sfsmisc'
Packages required but not available:
  'gtools', 'Rcpp', 'gmp', 'ggplot2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'OpenImageR', 'FD', 'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AER', 'Formula', 'plm', 'sandwich', 'lmtest', 'mlogit', 'dfidx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'e1071', 'rgl', 'R2HTML'

Packages suggested but not available for checking: 'mlbench', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'clusterCrit', 'copula', 'WeightedCluster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sp', 'spdep'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ClusterR', 'copula', 'dplyr', 'magrittr', 'tidyr', 'ggplot2',
  'rlang', 'knitr'

Packages suggested but not available for checking:
  'ggExtra', 'rmarkdown', 'testthat', 'Hmisc', 'tictoc', 'spelling',
  'corrplot', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'mclust', 'reshape2', 'msm', 'mvtnorm', 'truncnorm',
  'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RColorBrewer', '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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'PCAmixdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BAMBI', 'igraph', 'purrr', 'ggplot2', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'cowplot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flexclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rARPACK', 'tibble', 'corpcor', 'GGally', 'fpc', 'dplyr',
  'plyr', 'ggrepel', 'ca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggraph', 'checkmate', 'igraph', 'dplyr', 'ggplot2', 'viridis',
  'rlang', 'tidygraph', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'SingleCellExperiment', 'Seurat',
  'covr', 'SummarizedExperiment', 'pkgdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'stringi', 'stringr', 'stringdist', 'igraph',
  'assertthat', 'forcats', 'rlang', 'tidygraph', 'ggraph', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'klaR', 'dplyr', 'psycho'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
braycurtis: no visible global function definition for 'as.dist'
czekanowski: no visible global function definition for 'as.dist'
findComplementaryIndices: no visible global function definition for
  'na.omit'
genSimilarityProfile: no visible global function definition for 'dist'
simprof: no visible global function definition for 'dist'
simprof: no visible global function definition for 'hclust'
simprof.plot : <local> : colorizer: no visible global function
  definition for 'is.leaf'
simprof.plot: no visible global function definition for 'rainbow'
simprof.plot: no visible global function definition for 'dendrapply'
simprof.plot: no visible global function definition for 'as.dendrogram'
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'iterators', 'plyr', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mclust', 'BMA', 'foreach', 'iterators'

Packages suggested but not available for checking:
  'doParallel', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'mvtnorm', 'Rmixmod', 'VarSelLCM', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'moe430a.db', 'RankAggreg',
  'kohonen', 'mclust'
Packages unavailable to check Rd xrefs: 'kohonen', 'mclust', 'RankAggreg'
Errors in running code in vignettes:
when running code in 'clValid.Rnw'
  ...
+     CEW .... [TRUNCATED] 
Loading required package: RankAggreg
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'RankAggreg'

> plot(CEWS)

  When sourcing 'clValid.R':
Error: error in evaluating the argument 'x' in selecting a method for function 'plot': object 'CEWS' not found
Execution halted

  'clValid.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'clValid.Rnw' using Sweave
Loading required package: cluster
Read 7 items
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Biobase'
Loading required package: RankAggreg
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'RankAggreg'

Error: processing vignette 'clValid.Rnw' failed with diagnostics:
 chunk 25 (label = RankAggFig) 
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'plot': object 'CEWS' not found

--- failed re-building 'clValid.Rnw'

SUMMARY: processing the following file failed:
  'clValid.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'data.table', 'ggplot2', 'lubridate', 'optimx', 'Rcpp',
  'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking:
  'covr', 'future', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RUnit'
cma_es: no visible global function definition for 'rnorm'
f_rand: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ParamHelpers', 'BBmisc', 'checkmate', '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', 'scales', 'reshape2', 'stringr'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'earth', 'Rmosek', 'stringr', 'AUC', 'Ryacas0'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Matching', 'lmtest', 'multiwayvcov', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for 'cov'
alpha.curve: no visible global function definition for 'text'
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
Packages required but not available:
  'magrittr', 'x3ptools', 'dplyr', 'ggplot2', 'imager', 'purrr', 'zoo',
  'stringr', 'assertthat', 'scales', 'ggnewscale', 'quantreg',
  'tibble', 'tidyr', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'testthat', 'DT', 'magick', 'rgl',
  'covr', 'gridExtra', 'cowplot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'purrr', 'R.utils', 'rlang', 'testthat', 'usethis'

Packages suggested but not available for checking:
  'cli', 'covr', 'knitr', 'processx', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'hierNet', 'sparsenet', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rsparse', 'recommenderlab'

Package which this enhances but not available for checking: 'SparseM'
Package required but not available: 'quadprog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'progress', 'RJSONIO'

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', 'devtools', 'markdown', 'roxygen2'
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
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'ggplot2', 'twang', 'sandwich'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'chron'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'fields', 'FNN', 'ncdf4', 'rainfarmr', 'raster', 'sp',
  'progress', 'trend', 'SearchTrees'

Packages suggested but not available for checking:
  'cmsaf', 'cmsafvis', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cmsafops', 'cmsafvis', 'colourpicker', 'colorspace', 'fields',
  'FNN', 'mapproj', 'maps', 'maptools', 'ncdf4', 'R.utils', 'raster',
  'rworldxtra', 'shiny', 'shinyFiles', 'shinyjs', 'shinythemes', 'sp',
  'data.table', 'SearchTrees'

Packages suggested but not available for checking: 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'animation', 'assertthat', 'cmsafops', 'colorspace', 'countrycode',
  'fields', 'mapproj', 'maps', 'maptools', 'ncdf4', 'png', 'progress',
  'raster', 'rworldxtra', 'sp', 'yaml', 'RColorBrewer', 'rasterVis',
  'gridExtra', 'SearchTrees', 'rgdal'

Packages suggested but not available for checking:
  'plotKML', 'rnaturalearth', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'shinyMatrix', 'epitools', 'caret', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'magrittr', 'readr', 'rlang', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'generics', 'ggplot2', 'kSamples', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'lintr', 'purrr', 'rmarkdown', 'spelling', 'testthat',
  'tidyr', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'emulator', 'elliptic'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'dplyr', 'htmltools', 'htmlwidgets', 'jsonlite', 'magrittr',
  'r2d3', 'readxl', 'stringr', 'testthat', 'tibble', 'widgetframe'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cna', 'Rcpp', 'matrixStats', 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'matrixStats', 'car'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'hypergeo'

Packages suggested but not available for checking:
  'rmutil', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgl', 'tkrplot', 'tcltk2', 'shapes', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adlift', 'miscTools', 'nlt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adlift', 'nlt', 'CNLTreg', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'seqinr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaps', 'latticeExtra'

Packages suggested but not available for checking:
  'knitr', 'shiny', 'shinycssloaders', 'readxl', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mclust', 'rlecuyer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ape', 'PhyloMeasures'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', 'Rcpp', 'BH'

Package suggested but not available for checking: 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'vegan', 'rstantools', 'BH', 'RcppEigen',
  'RcppParallel', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'reshape2', 'magrittr', 'jointseg', 'shiny',
  'RCurl', 'foreach', 'GenomicInteractions', 'OpenImageR', 'biomaRt',
  'matrixStats', 'plyr', 'data.table', 'dplyr', 'numbers',
  'rtracklayer', 'doParallel', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'remotes', 'pwr', 'ComplexHeatmap', 'rmarkdown', 'HiCseg',
  'igraph', 'visNetwork', 'circlize', 'plotly', 'InteractionSet',
  'GenomicRanges', 'GenomicFeatures', 'IRanges', 'rslurm',
  'shinythemes', 'shinycssloaders', 'DT', 'logging', 'heatmaply',
  'S4Vectors', 'BiocManager', 'shinyjs', 'htmltools', 'htmlwidgets',
  'GenomeInfoDb', 'BSgenome.Hsapiens.UCSC.hg19', 'tibble', 'smoothie'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'digest', 'R6', 'Rcpp', 'rehh', 'scrm', 'RcppArmadillo'

Packages suggested but not available for checking:
  'abc', 'knitr', 'phyclust', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'coda', 'phangorn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'gtools', 'rvest', 'xml2', 'jsonlite', 'RCurl', 'rlang',
  'magrittr', 'lubridate', 'stringr', 'tidyr', 'purrr', 'dplyr',
  'ggplot2', 'tibble'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gtable', 'gridExtra', 'rlang', 'crayon', 'backports'

Packages suggested but not available for checking:
  'MatchIt', 'WeightIt', 'twang', 'Matching', 'optmatch', 'ebal',
  'CBPS', 'designmatch', 'optweight', 'mice', 'MatchThem', 'cem',
  'mlogit', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'snowfall', 'lars', 'ridge', 'tree', 'randomForest'
'library' or 'require' calls in package code:
  'lars' 'randomForest' 'ridge' 'snowfall' 'tree'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
COBRA : COBRA.lars: no visible global function definition for 'lars'
COBRA : COBRA.lars: no visible global function definition for
  'predict.lars'
COBRA : COBRA.tree: no visible global function definition for 'tree'
COBRA : COBRA.tree: no visible global function definition for
  'as.formula'
COBRA : COBRA.tree: no visible global function definition for 'predict'
COBRA : COBRA.ridge: no visible global function definition for
  'linearRidge'
COBRA : COBRA.ridge: no visible global function definition for
  'as.formula'
COBRA : COBRA.ridge: no visible global function definition for
  'predict'
COBRA : COBRA.randomForest: no visible global function definition for
  'randomForest'
COBRA : COBRA.randomForest: no visible global function definition for
  'predict'
COBRA: no visible global function definition for 'sfInit'
COBRA: no visible global function definition for 'sfLibrary'
COBRA: no visible global function definition for 'sfExportAll'
COBRA: no visible global function definition for 'sfSapply'
COBRA: no visible global function definition for 'sfStop'
COBRA: no visible global function definition for 'write.table'
COBRA: no visible global function definition for 'pdf'
COBRA: no visible global function definition for 'points'
COBRA: no visible global function definition for 'legend'
COBRA: no visible global function definition for 'abline'
COBRA: no visible global function definition for 'lines'
COBRA: no visible global function definition for 'dev.off'
COBRA: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  abline as.formula dev.new dev.off lars legend linearRidge lines pdf
  points predict predict.lars randomForest sfExportAll sfInit sfLibrary
  sfSapply sfStop tree write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "points")
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages required but not available: 'SparseM', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'fpc', 'glmnet', 'pheatmap', 'RColorBrewer', 'sparcl'

Packages suggested but not available for checking:
  'knitr', 'mclust', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'dplyr', 'tidyr', 'tibble', 'ggplot2',
  'magrittr', 'ggtern', 'forcats', 'DT'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'copula', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'limma'
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
Package required but not available: 'vegan'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

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 '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: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SQUAREM', 'future', 'future.apply'

Packages suggested but not available for checking:
  'knitr', 'ggtern', 'gtools', 'remotes', 'testthat', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rmdpartials', 'forcats', 'vctrs', 'ggplot2', 'stringr', 'rlang',
  'dplyr', 'tidyr', 'tidyselect', 'jsonlite', 'haven', 'purrr',
  'tibble', 'glue', 'likert', 'knitr', 'skimr', 'htmltools',
  'labeling', 'labelled'

Packages suggested but not available for checking:
  'testthat', 'DT', 'shinytest', 'lme4', 'rmarkdown', 'rstudioapi',
  'shiny', 'miniUI', 'roxygen2', 'webshot', 'rio', 'psych', 'future',
  'ufs', 'userfriendlyscience'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'beepr', 'cli'

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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'graph', 'XML'

Packages suggested but not available for checking:
  'Rgraphviz', 'RUnit', 'knitr', 'highlight', 'RJSONIO', 'RCurl',
  'Rcpp'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'commonmark', 'crul', 'desc', 'gert', 'gh', 'jsonlite', 'magrittr',
  'memoise', 'pingr', 'pkgbuild', 'purrr', 'remotes', 'sessioninfo',
  'urltools', 'xml2', 'cli'

Packages suggested but not available for checking:
  'covr', 'details', 'dplyr', 'jsonld', 'jsonvalidate', 'knitr',
  'printr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tibble'
Note: found 6 marked UTF-8 strings
Package suggested but not available for checking: 'vegan'
Packages suggested but not available for checking:
  'deSolve', 'bvpSolve', 'testthat'
Package unavailable to check Rd xrefs: 'deSolve'
Packages required but not available:
  'data.table', 'decoder', 'generics', 'tibble'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'writexl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'checkmate', 'dplyr', 'kableExtra', 'knitr', 'magrittr', 'readr',
  'rlang', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'REDCapR', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'igraph', 'magrittr', 'plyr', 'visNetwork', 'reshape2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'wTO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fractional'

Packages suggested but not available for checking:
  'knitr', 'dplyr', 'car', 'ggplot2', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/codingMatrices.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'permute', 'vegan'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'pillar', 'reshape2', 'devtools',
  'dplyr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rsem', 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'reshape2', 'useful', 'dplyr', 'dygraphs',
  'tibble', 'magrittr', 'purrr', 'plotly'

Packages suggested but not available for checking:
  'testthat', 'covr', 'glmnet', 'maxLik', 'xgboost', 'workflows',
  'parsnip', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/coenocliner.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/coenocliner.Rnw'
(Is a VignetteBuilder field missing?)
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
Malformed Description field: should contain one or more complete sentences.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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', 'lazyeval', '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: 'gplots', 'stringr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'cubature', 'RcppGSL'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'graph', 'Rgraphviz', 'ggplot2', 'magrittr', '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:
  'shiny', 'yaml', 'config', 'shinyjs', 'httr', 'dplyr', 'base64enc',
  'jsonlite', 'paws'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'ggplot2', 'plotly', 'tidyr', 'doParallel',
  'foreach', 'openxlsx', 'forcats', 'epitools', 'zoo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'DT', 'gtools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Epi', 'cmprsk', 'ggplot2', 'DiagrammeR', 'DiagrammeRsvg', 'rsvg'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mstate', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'aphid', 'seqinr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'copula', 'gtools', 'locfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'ggplot2', 'data.table', 'curl', 'cli', 'crayon'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggthemes', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'plyr', 'coin', 'Rdpack', 'exactRankTests', 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'libcoin', 'matrixStats', 'modeltools', 'mvtnorm', 'multcomp'

Packages suggested but not available for checking:
  'xtable', 'e1071', 'vcd', 'TH.data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cointReg', 'matrixStats'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'checkmate', 'matrixStats'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nlsr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'lazyeval', 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'dplyr', 'plm', 'data.table', 'matrixStats', 'magrittr', 'fixest',
  'lfe', 'vars', 'weights', 'kit', 'RcppArmadillo', 'RcppEigen',
  'ggplot2', 'scales', 'microbenchmark', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'data.tree'

Packages suggested but not available for checking:
  'colorspace', 'RColorBrewer', 'dplyr', 'testthat', 'tibble'

Packages which this enhances but not available for checking:
  'knitr', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
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', 'stringr', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dlnm', 'VGAM'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/collin.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'spam', 'deSolve'

Packages suggested but not available for checking:
  'pomp', 'SparseM', 'subplex', 'trust', 'maxLik'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'vegan', 'network', 'latentnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rJava', 'Rcpp'

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', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'doParallel', 'purrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'ggplot2', 'snpStats', 'BMA', 'reshape'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'bindata', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'imager', 'magick', 'shiny', 'scales', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'covr', 'knitr', 'rmarkdown', 'devtools',
  'purrr', 'shinyBS'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'colorspace', 'gridGraphics', 'gtable'

Packages suggested but not available for checking:
  'knitr', 'reshape2', 'png', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'purrr', 'crayon'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'fansi', 'htmltools', 'data.table', 'testthat',
  'tibble', 'dplyr', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jpeg', 'png', 'clue', 'ape', 'emdist', 'scatterplot3d', 'plotly',
  'gplots', 'abind', 'magrittr', 'scales', 'qpdf', 'spatstat.geom'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fastICA'
cICA: no visible global function definition for 'mvfft'
cICA: no visible global function definition for 'ar.yw'
cICA: no visible global function definition for 'rnorm'
scICA: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
Running examples in 'coloredICA-Ex.R' failed
The error most likely occurred in:

> ### Name: cICA
> ### Title: colored Independent Component Analysis
> ### Aliases: cICA
> 
> ### ** Examples
> 
> ## Not run:
> 
> require(fastICA)
Loading required package: fastICA
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'fastICA'
> 
> T=256
> n1=16
> n2=16
> M=2
> 
> S1 = arima.sim(list(order=c(0,0,2),ma=c(1,0.25)),T)
> S2 = arima.sim(list(order=c(1,0,0), ar=-0.5),T,rand.gen = function(n, ...) (runif(n)-0.5)*sqrt(3))
> 
> A = rerow(matrix(runif(M^2)-0.5,M,M))
> W = solve(A)
> S=rbind(S1,S2)
> X = A %*% S
> 
> cica = cICA(X,tol=0.001)
[1] "Color ICA - Iteration 1: error is equal to 0.72534567538578"
[1] "Color ICA - Iteration 2: error is equal to 0.102655086460911"
[1] "Color ICA - Iteration 3: error is equal to 0.0292728412342725"
[1] "Color ICA - Iteration  4 : current Whittle likelihood( 355.740792732174 ) is smaller than previous one ( 356.501699985553 )."
[1] "Color ICA - Iteration 4: error is equal to 0.00177080770209836"
[1] "Color ICA - Iteration  5 : current Whittle likelihood( 355.735885896869 ) is smaller than previous one ( 356.501699985553 )."
[1] "Color ICA - Iteration 5: error is equal to 9.35742408500473e-05"
> ## scica = scICA(X,n1=n1,n2=n2,h=0.8,tol=0.001)
> fica = fastICA(t(X),2)
Error in fastICA(t(X), 2) : could not find function "fastICA"
Execution halted
Packages required but not available:
  'purrr', 'Rcpp', 'data.table', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown', 'testthat', 'covr', 'pkgdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'purrr', 'stringr', 'pixmap', 'tibble', 'treemap', 'rsvg', 'png',
  'jpeg', 'tiff', 'bmp', 'dplyr', 'plotly', 'magrittr', 'plotwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn2d: no visible global function definition for 'grid.text'
plotVenn2d: no visible global function definition for 'gpar'
plotVenn2d: no visible global function definition for 'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn3d: no visible global function definition for 'grid.text'
plotVenn3d: no visible global function definition for 'gpar'
plotVenn3d: no visible global function definition for 'grid.polygon'
plotVenn4d : getCommonEllipse: no visible global function definition
  for 'aggregate'
plotVenn4d : region.polygon: no visible global function definition for
  'head'
plotVenn4d : region.polygon: no visible global function definition for
  'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'gpar'
plotVenn4d: no visible global function definition for 'grid.text'
plotVenn4d: no visible global function definition for 'gpar'
plotVenn4d: no visible global function definition for 'pushViewport'
plotVenn4d: no visible global function definition for 'viewport'
plotVenn4d: no visible global function definition for 'grid.polygon'
plotVenn4d: no visible global function definition for 'upViewport'
resizeCircles: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'colorspace', 'ggplot2', 'magrittr', 'raster', 'scales', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'RColorBrewer', 'rmarkdown', 'sf', 'rnaturalearth', 'tigris'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'magick', 'purrr', 'dplyr', 'stringr', 'tibble', 'magrittr'

Package suggested but not available for checking: 'gifski'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'V8', 'stringr', 'ggplot2'

Packages suggested but not available for checking: 'scales', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
generateMonochromaticColors: no visible global function definition for
  'col2rgb'
generateMonochromaticColors: no visible global function definition for
  'rgb'
generateMonochromaticColors: no visible global function definition for
  'tail'
hsv2rgb: no visible global function definition for 'rgb'
rotational_dispersion: no visible global function definition for
  'col2rgb'
rotational_dispersion: no visible global function definition for
  'rgb2hsv'
tetradicColors: no visible global function definition for 'head'
triadicColors: no visible global function definition for 'head'
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'colorspace', 'gridExtra', 'TSP'

Packages suggested but not available for checking:
  'plotly', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for 'rgb'
rgb.tables: no visible global function definition for 'rgb'
ygobb: no visible global function definition for 'approx'
ygobb: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Hmisc', 'pracma', 'sp'

Package which this enhances but not available for checking: 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'kernlab', 'mvtnorm', 'vcd', 'shiny', 'shinyjs', 'ggplot2', 'dplyr',
  'scales', 'png', 'jpeg', 'knitr', 'rmarkdown', 'RColorBrewer',
  'rcartocolor', 'scico', 'viridis', 'wesanderson'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'ggplot2'
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
Errors in running code in vignettes:
when running code in 'hcl-colors.Rnw'
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'hcl-colors.Rnw'... failed to complete the test
Package required but not available: 'spacesXYZ'

Packages suggested but not available for checking:
  'rootSolve', 'quadprog', 'rgl', 'knitr', 'rmarkdown', 'spacesRGB',
  'microbenchmark', 'arrangements'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/blueflame.rnw'
   'inst/doc/convexity.rnw'
   'inst/doc/emulation.rnw'
   'inst/doc/gallery.rnw'
   'inst/doc/inversion.rnw'
   'inst/doc/lens-aging.rnw'
   'inst/doc/optimals.rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'XML', 'jsonlite', 'httr', 'png'

Packages suggested but not available for checking:
  'httptest', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'htmltools', 'htmlwidgets', 'jsonlite', 'miniUI', 'shiny',
  'shinyjs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rstudioapi', 'shinydisconnect'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH'

Packages suggested but not available for checking:
  'covr', 'microbenchmark', 'scales', 'testthat', 'viridisLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'corrplot', 'rgl'

VignetteBuilder package required for checking but not installed: 'knitr'
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
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'crayon'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'gdata', 'XML', 'clusterSim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'tinytest', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'corpcor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'lubridate', 'magrittr', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'spelling', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
competitive.test: no visible global function definition for 'runif'
selfcontained.test : fun2: no visible global function definition for
  'qchisq'
selfcontained.test: no visible global function definition for 'cov'
selfcontained.test: no visible global function definition for 'qchisq'
selfcontained.test: no visible global function definition for 'cor'
selfcontained.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'iterators', 'itertools', 'Rcpp'

Packages suggested but not available for checking:
  'combinat', 'foreach', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
'library' or 'require' calls in package code:
  'lattice' 'rgl'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'httr', 'jsonlite', 'R.utils', 'R6', 'yaml'

Packages suggested but not available for checking:
  'covr', 'curl', 'git2r', 'httptest', 'ps', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'reshape'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstudioapi', 'shiny'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'NonpModelCheck', 'ggplot2', 'gtools', 'mvtnorm', 'splines2',
  'truncnorm', 'rlang', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.externalCallerEnv: no visible binding for global variable
  '.methodsNamespace'
Undefined global functions or variables:
  .methodsNamespace
Running examples in 'commandr-Ex.R' failed
The error most likely occurred in:

> ### Name: Protocol-class
> ### Title: Protocol: Concrete Step in a Pipeline
> ### Aliases: class:Protocol Protocol-class Protocol parameters
> ###   parameters,Protocol-method stage stage,Protocol-method
> ###   method,Protocol-method pipeline,Protocol-method method perform
> ###   callNextProtocol protocolClass
> 
> ### ** Examples
> 
> setStage("average", intype = "numeric")
[1] "average"
> setProtocol("mean", fun = mean, parent = "average")
[1] "ProtoAverageMean"
> setProtocol("quantile", representation = list(probs = "numeric"),
+             fun = quantile, parent = "average")
[1] "ProtoAverageQuantile"
> 
> proto_avg_mean <- Protocol("average")
> proto_avg_mean <- Protocol("average", "mean")
> proto_avg_quantile <- Protocol("average", "quantile")
> proto_avg_quantile_075 <- Protocol("average", "quantile", probs = 0.75)
> 
> proto <- proto_avg_quantile_075
> proto
average (quantile)
> stage(proto)
Error in identical(ev, .methodsNamespace) : 
  object '.methodsNamespace' not found
Calls: stage -> stage -> .local -> force -> .externalCallerEnv
Execution halted
Packages required but not available:
  'vegan', 'ape', 'picante', 'adespatial', 'betapart', 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stringr'

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: 'rJava', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/CommonJavaJars.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/CommonJavaJars.Rnw'
(Is a VignetteBuilder field missing?)
Packages suggested but not available for checking:
  'curl', 'testthat', 'xml2'
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: 'pracma', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rscala', 'rJava', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'Rcpp', 'purrr', 'magrittr', 'diagram', 'GGally', 'useful',
  'ggplot2', 'reshape2', 'tuneR', 'wrassp', 'gtools', 'signal', 'plyr',
  'RColorBrewer', 'scales', 'abind', 'igraph', 'gtable',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'qpdf', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'checkmate', 'data.table'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ROCR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'plyr', 'fda', 'orthogonalsplinebasis', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
addxaxis: no visible global function definition for 'par'
addxaxis: no visible global function definition for 'axis'
addxaxis: no visible global function definition for 'mtext'
eplot: no visible global function definition for 'par'
eplot: no visible global function definition for 'axis'
eplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'proxy', 'clue'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'expm', 'data.table'

Packages suggested but not available for checking:
  'pcalg', 'InvariantCausalPrediction', 'glmnet', 'backShift', 'CAM',
  'kernlab', 'mboost', 'bnlearn', 'testthat', 'huge', 'flare'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
compareC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Packages required but not available:
  'copula', 'ggplot2', 'rootSolve', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'data.table', 'magrittr', 'htmlTable', 'openxlsx', 'tidyr',
  'stringr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'futile.logger', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'HardyWeinberg', 'rmarkdown', 'knitr', 'kableExtra', 'chron',
  'writexl', 'flextable', 'officer'

Packages suggested but not available for checking:
  'tcltk2', 'shiny', 'shinyBS', 'shinyjs', 'shinyjqui', 'shinythemes',
  'shinyWidgets', 'shinydashboardPlus', 'DT', 'readxl', 'haven'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'R6'

Packages suggested but not available for checking:
  'plyr', 'progress', 'testthat', 'covr', 'knitr', 'ggplot2', 'GGally',
  'snow', 'rmarkdown', 'reshape', 'tibble', 'lhs', 'DiceKriging',
  'DiceOptim', 'reshape2', 'microbenchmark'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CIFsmry', 'cmprsk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'isotone'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'survRM2', 'TSHRC', 'muhaz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'bio3d', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'numDeriv', 'fExtremes', 'actuar', 'VGAM', 'rmutil', 'PearsonDS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'comperes', 'dplyr', 'Rcpp', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'rlang', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'antitrust', 'trade', 'shiny', 'rhandsontable', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Benchmarking', 'psych', 'lpSolve', 'spdep', 'Hmisc', 'GPArotation',
  'nonparaeff', 'smaa', 'np'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'dplyr', 'tibble', 'progress', 'stringr', 'zeallot'

Packages suggested but not available for checking:
  'lubridate', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'combinat', 'shiny'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package required but not available: 'expm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'patchwork', 'scales', 'colorspace'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'tibble', 'ggplot2movies',
  'vdiffr', 'jsonlite', 'data.table'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'robustbase', 'ggplot2', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'laGP'

VignetteBuilder package required for checking but not installed: 'R.rsp'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'codalm', 'Directional', 'doParallel', 'emplik', 'FlexDir',
  'foreach', 'glmnet', 'mda', 'mixture', 'NlcOptim', 'pchc', 'RANN',
  'Rfast', 'Rfast2', 'sn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tensorA', 'robustbase', 'bayesm'

Packages suggested but not available for checking:
  'rgl', 'combinat', 'energy', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'otsad', 'tsoutliers', 'forecast', 'anomalize', 'dplyr', 'tibble',
  'rlang', 'pracma', 'dobin', 'ICS', 'fastICA', 'gridExtra', 'ggplot2',
  'tidyr', 'kableExtra'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tourr', 'stringr', 'broom', 'rgdal'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'hypergeo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RandomFields', 'spam', 'scatterplot3d', 'fields', 'mapproj', 'maps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'tinytest', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'fs', 'httr', 'janitor', 'lubridate', 'purrr', 'rlang',
  'readr', 'rvest', 'sf', 'stringr', 'tibble', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vegan'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'bookdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'magrittr', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'dplyr'
'LazyData' is specified without a 'data' directory
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
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
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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:
  'V8', 'sf', 'magrittr', 'jsonlite', '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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rlang', 'stringr', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rglpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompQuadForm', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bcaboot', 'dplyr', 'flextable', 'ggplot2', 'knitr', 'metafor',
  'officer', 'pbmcapply', 'ProfileLikelihood', 'scales', 'colorspace',
  'survminer', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'lme4', 'covr', 'roxygen2', 'spelling', 'testthat', 'rmarkdown',
  'Lock5Data', 'carData', 'bench', 'rms', 'brms', 'rstan', 'rstanarm',
  'bayesplot', 'vdiffr', 'ggtext', 'daewr', 'svglite', 'data.table',
  'simstudy', 'patchwork', 'cowplot', 'reprex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gridExtra', 'gtable', 'htmlTable', 'htmltools', 'knitr',
  'magrittr', 'openxlsx', 'rmarkdown', 'rlang', 'scales', 'tibble',
  'tidyselect'

Packages suggested but not available for checking:
  'promises', 'shiny', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'numDeriv', 'rootSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'randomForest', 'quantregForest', 'lawstat', 'RPtests', 'caTools',
  'kernlab', 'pracma', 'mize'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BayesFactor', 'knitr', 'xtable', 'psych', 'effsize', 'shiny'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'uuid'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'evd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'statmod'

Packages suggested but not available for checking:
  'csampling', 'marg', 'nlreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for 'approx'
select_kmax: no visible global function definition for 'median'
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
Packages required but not available: 'np', 'doParallel', 'doRNG', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'condMVNorm', 'matrixNormal', 'tmvmixnorm', 'tmvtnorm', 'truncnorm'

Packages suggested but not available for checking:
  'formatR', 'knitr', 'rmarkdown', 'roxygen2', 'sessioninfo',
  'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'assertthat', 'bigrquery', 'DBI'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'whisker', 'testthat', 'RSQLite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'RColorBrewer', 'ggplot2', 'scales', 'DendSer', 'plyr',
  'colorspace', 'gower'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'hdrcde', 'scagnostics', 'keras', 'kernlab',
  'mclust', 'ks', 'randomForest', 'parsnip', 'mlr', 'C50',
  'bartMachine', 'caret', 'e1071', 'gbm', 'glmnet', 'glmnetUtils',
  'mlr3', 'tree', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'RColorBrewer', 'shiny', 'scagnostics', 'hdrcde', 'gplots', 'TSP',
  'DendSer', 'testthat'
Running examples in 'condvis-Ex.R' failed
The error most likely occurred in:

> ### Name: makepath
> ### Title: Make a default path for conditional tour
> ### Aliases: makepath
> 
> ### ** Examples
> 
> d <- data.frame(x = runif(500), y = runif(500))
> plot(d)
> mp1 <- makepath(d, 5)
Error in makepath(d, 5) : requires package 'TSP'
Execution halted
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: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'markdown', 'plyr', 'xtable', 'ggplot2'

Package suggested but not available for checking: 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/confidence.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ini', 'R6'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'yaml'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'ini', 'yaml', 'RcppTOML', 'stringr', 'glue'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'crayon'
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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: 'rlang', 'memoise'

Packages suggested but not available for checking:
  'covr', 'crayon', 'dplyr', 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'askpass', 'commonmark', 'curl', 'glue', 'httr', 'knitr', 'miniUI',
  'purrr', 'rmarkdown', 'rstudioapi', 'shiny', 'stringi', 'xml2', 'R6',
  'rlang'

Packages suggested but not available for checking:
  'mockery', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'randomForest', 'foreach', 'doParallel', 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'metafor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gridExtra', 'scales', 'Rmpfr', 'dplyr', 'tidyr', 'ggplot2',
  'magrittr', 'stringr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat', 'broom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'statmod', 'STAR', 'fitdistrplus', 'pracma', 'rootSolve'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'penalized', 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Ternary'

Packages suggested but not available for checking:
  'ape', 'bookdown', 'knitr', 'phangorn', 'Quartet', 'rmarkdown',
  'TreeSearch', 'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pracma', 'geigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
conicPlot: no visible global function definition for 'palette'
conicPlotAsymptotes: no visible global function definition for
  'palette'
conicPlotAsymptotes: no visible global function definition for 'abline'
conicPlotAxes: no visible global function definition for 'palette'
conicPlotAxes: no visible global function definition for 'abline'
plotDegenerateConic: no visible global function definition for 'points'
plotDegenerateConic: no visible global function definition for 'abline'
plotEllipsis: no visible global function definition for 'lines'
plotEllipsis: no visible global function definition for 'points'
plotHyperbola: no visible global function definition for 'lines'
plotHyperbola: no visible global function definition for 'points'
plotParabola: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'stringdist', 'dplyr', 'stringr', 'ppcor', 'mitools',
  'miceadds'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'snow', 'Rmpi'
Malformed Title field: should not end in a period.
'library' or 'require' call to 'parallel' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Rmpi' 'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for 'makeCluster'
ConjointChecks: no visible global function definition for
  'clusterSetRNGStream'
ConjointChecks: no visible global function definition for
  'clusterApply'
ConjointChecks: no visible global function definition for 'stopCluster'
omni.check: no visible global function definition for 'runif'
omni.check: no visible global function definition for 'quantile'
plot.checks: no visible global function definition for 'mtext'
plot.checks: no visible global function definition for 'text'
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Packages required but not available:
  'AlgDesign', 'fpc', 'broom', 'ggplot2', 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DBI', 'pins', 'dplyr', 'dbplyr', 'uuid', 'rscontract'

Packages suggested but not available for checking:
  'RSQLite', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'igraph', 'mcmc'
Package unavailable to check Rd xrefs: 'igraph'
Running examples in 'ConnMatTools-Ex.R' failed
The error most likely occurred in:

> ### Name: d.rel.conn.multinomial.unnorm
> ### Title: Calculates unnormalized probability density for relative
> ###   connectivity values from multiple distinct sites
> ### Aliases: d.rel.conn.multinomial.unnorm
> 
> ### ** Examples
> 
> library(ConnMatTools)
> 
> ps <- c(0.7,0.5) # Fraction of eggs "marked" at each source site
> ks <- c(4,5) # Number of marked settlers among sample from each source site
> n.sample <- 20 # Total sample size.  Must be >= sum(ks)
> 
> 
> phis0 = runif(3,min=0.05)
> phis0 = phis0 / sum(phis0)
> phis0 = phis0[1:2] # Don't include relative connectivity of unknown sites
> 
> nbatch=1e4
> 
> library(mcmc)
Error in library(mcmc) : there is no package called 'mcmc'
Execution halted
Running 'test.connectivity_estimation.R'
  Running 'test.connectivity_estimation.beta.prior.R'
  Running 'test.connectivity_estimation.distributions.R'
  Running 'test.connectivity_estimation.multinomial.R'
Running the tests in 'tests/test.connectivity_estimation.multinomial.R' failed.
Last 13 lines of output:
  > 
  > ps <- c(0.7,0.5) # Fraction of eggs "marked" at each source site
  > ks <- c(4,5) # Number of marked settlers among sample from each source site
  > n.sample <- 20 # Total sample size.  Must be >= sum(ks)
  > 
  > 
  > phis0 = runif(3,min=0.05)
  > phis0 = phis0 / sum(phis0)
  > phis0 = phis0[1:2] # Don't include relative connectivity of unknown sites
  > 
  > nbatch=1e4
  > 
  > library(mcmc)
  Error in library(mcmc) : there is no package called 'mcmc'
  Execution halted
Packages required but not available:
  'psych', 'mvtnorm', 'checkmate', 'assertthat'

Packages suggested but not available for checking:
  'testthat', 'psychTools', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'abind', 'cowplot', 'ComplexHeatmap', 'dendextend',
  'dplyr', 'ggplot2', 'ggrepel', 'gridExtra', 'irlba', 'leidenAlg',
  'magrittr', 'Matrix.utils', 'N2R', 'R6', 'reshape2', 'rlang',
  'Rtsne', 'sccore', 'Rcpp', 'RcppArmadillo', 'RcppEigen',
  'RcppProgress'

Packages suggested but not available for checking:
  'AnnotationDbi', 'BiocParallel', 'conosPanel', 'DESeq2', 'entropy',
  'ggrastr', 'GO.db', 'jsonlite', 'knitr', 'org.Hs.eg.db',
  'org.Mm.eg.db', 'p2data', 'pagoda2', 'pbapply', 'PMA', 'pROC',
  'plyr', 'rhdf5', 'rmarkdown', 'rmumps', 'Seurat', 'shinycssloaders',
  'SummarizedExperiment', 'testthat', 'tibble', 'uwot', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'matrixStats', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'reshape', 'ggplot2', 'stringr', 'rlang', 'ggrepel'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'sp', 'fields', 'geosphere', 'rgdal', 'rgeos', 'tibble',
  'writexl', 'snow', 'doSNOW', 'foreach', 'rnaturalearth', 'sf'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'rnaturalearthdata', 'alphahull'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coneproj'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'rlist', 'proxy', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'forecast', 'rlang', 'nloptr', 'FME', 'MCMCpack',
  'Rsolnp', 'DEoptim', 'dfoptim', 'GA', 'GenSA', 'Metrics', 'ggplot2',
  'adaptMCMC', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'errors', 'units', 'quantities', '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: 'data.table'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'devtools', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'spatialCovariance', 'rgeos', 'RandomFields'

Package suggested but not available for checking: 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'caroline', 'gtools', 'foreach',
  'doParallel', 'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'maps'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'countrycode', 'ggplot2', 'knitr', 'rmarkdown', 'spelling',
  'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'ape', 'data.table', 'doParallel', 'foreach', 'igraph', 'lubridate',
  'raster', 'rgdal', 'rgeos', 'sp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'R6'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mixture', 'mnormt', 'mclust', 'caret', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'openssl', 'httr', 'curl', 'fs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'thor', 'vroom', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'data.table', 'R.devices', 'foreach', 'doParallel',
  'itertools', 'iterators', 'Formula', 'rjson'

Packages suggested but not available for checking:
  'testthat', 'RCurl', 'splitstackshape', 'covr', 'knitr', 'here',
  'rmarkdown', 'devtools', 'ggplot2', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rje'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'BMS', 'gtools', 'tseries', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geometry', 'Rcpp', 'reshape', 'plyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
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  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'ContourFunctions-Ex.R' failed
The error most likely occurred in:

> ### Name: cf
> ### Title: Make contour plot from data or function
> ### Aliases: cf
> 
> ### ** Examples
> 
> cf(function(x){x[1]^2 - x[2]})
> x <- runif(20)
> y <- runif(20)
> z <- exp(-(x-.5)^2-5*(y-.5)^2)# + rnorm(20,0,.05)
> cf(x,y,z)
Error in loadNamespace(x) : there is no package called 'laGP'
Calls: cf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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: 'interp', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sandwich', 'rms'

Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'dplyr', 'ggplot2', 'tidyr', 'rmarkdown',
  'testthat', 'covr', 'geepack'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'rlang', 'magrittr', 'gh'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pracma', 'expm', 'signal'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'pryr', 'extraDistr', 'dplyr', 'tidyr', 'ggplot2', 'RColorBrewer',
  'SHELF', 'shiny'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lmtest', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'eurostat', 'tidyr', 'rlang', 'purrr',
  'caTools', 'broom', 'stringr', 'rmarkdown', 'ggpubr'

Packages suggested but not available for checking:
  'devtools', 'formattable', 'gridExtra', 'knitr', 'kableExtra',
  'magrittr', 'readr', 'readxl', 'tidyverse', 'rvest', 'testthat',
  'utf8'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'miniUI', 'DT', 'rstudioapi'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'phytools', 'ape', 'geiger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'JuliaCall', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'plotrix'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survey'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'IC2', 'vardpoor', 'laeken', 'DBI',
  'RODBC', 'RSQLite', 'srvyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ellipse', 'fields', 'plotrix', 'StatMatch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'seqinr', 'igraph', 'bigmemory', 'foreach', 'pryr', 'knitr',
  'doParallel'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'reshape2', 'gmp', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'data.table', 'pROC', 'mltools', 'plyr', 'ggplot2',
  'ClustGeo', 'wesanderson', 'RcppArmadillo'

Packages suggested but not available for checking: 'ggtree', 'imager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'geometry', 'rcdd', 'gtools'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lpSolveAPI', 'ggplot2', 'GameTheory', 'dplyr', 'kappalab', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'memuse'

Package which this enhances but not available for checking: 'slam'
Packages required but not available: 'igraph', 'optrees', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geosphere', 'ggplot2', 'raster', 'rgbif', 'rgeos', 'rgdal',
  'rnaturalearth', 'sp', 'tidyselect'

Packages suggested but not available for checking:
  'covr', 'countrycode', 'knitr', 'maps', 'magrittr', 'paleobioDB',
  'rmarkdown', 'rnaturalearthdata', 'testthat', 'viridis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lmomco', 'randtoolbox'

Package suggested but not available for checking: 'copula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mcmcse', 'numDeriv', 'Rcpp', 'spam', 'RcppArmadillo'

Package suggested but not available for checking: 'pbapply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'copula', 'msm', 'copBasic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mnormt'
Running examples in 'copent-Ex.R' failed
The error most likely occurred in:

> ### Name: ci
> ### Title: Conditional independence test with copula entropy
> ### Aliases: ci
> ### Keywords: conditional independence
> 
> ### ** Examples
> 
> 
> library(copent)
> library(mnormt)
Error in library(mnormt) : there is no package called 'mnormt'
Execution halted
Running 'test1copent.R'
Running the tests in 'tests/test1copent.R' failed.
Complete output:
  > library(mnormt)
  Error in library(mnormt) : there is no package called 'mnormt'
  Execution halted
Packages required but not available: 'maps', 'abind', 'fields', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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: 'gsDesign', 'digest', 'plyr', 'proto'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cordillera', 'smacof', 'minqa', 'pso', 'scatterplot3d', 'NlcOptim',
  'Rsolnp', 'dfoptim', 'subplex', 'cmaes', 'crs', 'nloptr', 'rgenoud',
  'GenSA'

Packages suggested but not available for checking:
  'testthat', 'R.rsp', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'copula', 'corpcor', 'flexsurv', 'icenReg', 'magrittr',
  'plotly', 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'ggplot2', 'plyr', 'reshape2'

Packages suggested but not available for checking:
  'knitr', 'loo', 'Rmisc', 'httr', 'bayesplot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'copula', 'vines', 'mvtnorm', 'truncnorm'

Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'colorspace', 'gsl', 'ADGofTest', 'stabledist', 'mvtnorm', 'pcaPP',
  'pspline', 'numDeriv'

Packages suggested but not available for checking:
  'sfsmisc', 'scatterplot3d', 'Rmpfr', 'bbmle', 'knitr', 'rmarkdown',
  'abind', 'crop', 'gridExtra', 'lcopula', 'mev', 'mvnormtest',
  'partitions', 'polynom', 'qrng', 'randtoolbox', 'rugarch', 'Runuran',
  'tseries', 'VGAM', 'VineCopula', 'zoo'

Packages which this enhances but not available for checking:
  'nor1mix', 'copulaData'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvinecopulib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'statmod', 'matlab', 'tensor', 'mc2d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'mirt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'Rtsne', 'scatterplot3d'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'htmltools'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'CRF', 'igraph'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'BiocParallel', 'matrixcalc', 'mpmi',
  'fitdistrplus'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'Cairo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mcc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dbscan', 'yesno'

Package suggested but not available for checking: 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'pcaPP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'igraph', 'oro.dicom', 'plyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rJava', 'naturalsort'

Packages suggested but not available for checking:
  'testthat', 'mockr', 'StatMatch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotrix', 'rpart.plot'

Package suggested but not available for checking: 'ExplainPrediction'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rJava', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
advanceRNG: no visible global function definition for 'runif'
randomEventMoves: no visible global function definition for 'runif'
randomRescaledEventMoves: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  'write.table'
pvalue_calculator: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'ape', 'nloptr', 'GenSA', 'expm', 'numDeriv', 'corpcor', 'phangorn',
  'viridis', 'Rmpfr', 'igraph', 'phytools'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gplots', 'RColorBrewer', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'limma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'optimr', 'VGAM', 'numDeriv', 'ggplot2', 'trust', 'dplyr',
  'magrittr', 'rmutil', 'detectseparation', 'scales', 'phyloseq'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'limma', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'minpack.lm', 'ranger', 'SpatialTools',
  'vcd'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'prettydoc', 'rmarkdown', 'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'palasso'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

Packages which this enhances but not available for checking:
  'RColorBrewer', 'mvtnorm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'plyr', 'gganimate', 'ggplot2', 'gridExtra', 'qicharts2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Packages suggested but not available for checking:
  'DT', 'dplyr', 'knitr', 'plotly', 'readr', 'remotes', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rlang'

Packages suggested but not available for checking:
  'knitr', 'later', 'magrittr', 'promises', 'reticulate', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'RColorBrewer', 'rlist'

Packages suggested but not available for checking:
  'unittest', 'stringi', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'ggplot2', 'lubridate', 'magrittr', 'padr',
  'plyr', 'RColorBrewer', 'rlang', 'rmarkdown', 'scales', 'shiny',
  'shinydashboard', 'shinyjs', 'shinyWidgets', 'stringi', 'stringr',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'janeaustenr', 'shinytest', 'sotu', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 1187 marked UTF-8 strings
Package required but not available: 'osDesign'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'utf8'

Packages suggested but not available for checking: 'knitr', 'testthat'

Packages which this enhances but not available for checking:
  'quanteda', 'tm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wordcloud', 'SnowballC', 'stringi', 'Rcpp', 'R6', 'udpipe',
  'digest', 'data.table', 'quanteda', 'igraph', 'tokenbrowser',
  'RNewsflow', 'pbapply', 'rsyntax', 'RcppProgress'

Packages suggested but not available for checking:
  'testthat', 'tm', 'topicmodels', 'knitr', 'rmarkdown', 'gender'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'fields', 'mmand', 'colorspace', 'profr',
  'xtable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp', 'testthat', 'rgl'

VignetteBuilder package required for checking but not installed: 'R.rsp'

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.
Packages required but not available:
  'combinat', 'geepack', 'dirmult', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LinkingTo' for
  'Rcpp' 'RcppArmadillo'
are unused as they have no 'include' directory
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'magrittr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ICC', 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'LFDR.MLE', 'LFDREmpiricalBayes', 'ProData'
Packages required but not available: 'XML', 'digest', 'bitops'

Packages suggested but not available for checking:
  'xcms', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'diagram', 'rgl', 'data.table', 'ellipse', 'gplots'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/corregp.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rlang', 'recipes', 'magrittr', 'plotly', 'tibble',
  'dplyr', 'tidyr', 'ggrepel', 'stringr', 'forcats', 'purrr', 'cli',
  'crayon', 'rstudioapi'

Packages suggested but not available for checking:
  'scales', 'knitr', 'rmarkdown', 'covr', 'lubridate', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayestestR', 'effectsize', 'insight', 'parameters'

Packages suggested but not available for checking:
  'BayesFactor', 'dplyr', 'energy', 'forcats', 'ggcorrplot', 'ggplot2',
  'gt', 'Hmisc', 'knitr', 'lme4', 'polycor', 'ppcor', 'psych',
  'rmarkdown', 'rmcorr', 'rstanarm', 'see', 'spelling', 'testthat',
  'tidyr', 'wdm', 'WRS2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rmpfr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'seriation'

Packages suggested but not available for checking:
  'gridBase', 'knitr', 'psych', 'rmarkdown', 'sfsmisc', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'visNetwork', 'ingredients', 'htmltools', 'ggplot2', 'knitr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'DALEX', 'gbm', 'ranger', 'spelling', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'RColorBrewer', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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', 'seriation', 'purrr', 'tibble', 'ggrepel',
  'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dbplyr', 'DBI', 'RSQLite',
  'sparklyr', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for 'cor'
corr.Qmatrix: no visible global function definition for 'cor.test'
summarise.Fst: no visible global function definition for 'cor'
summarise.Fst: no visible global function definition for 'sd'
summarise.lnPD: no visible global function definition for 'sd'
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Packages required but not available:
  'BinNonNor', 'BinOrdNonNor', 'GenOrd', 'moments', 'mvtnorm', 'psych'

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.
Last 13 lines of output:
  > # 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:
  'igraph', 'clusterGeneration', 'Biobase', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dist: no visible global function definition for 'quantile'
edgecount: no visible global function definition for 'reshape'
edgecutoff: no visible global function definition for 'boxplot'
edgecutoff: no visible global function definition for 'sd'
edgecutoff: no visible global function definition for 'median'
edgecutoff: no visible global function definition for 'IQR'
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'gplots', 'knitr', 'pbapply', 'plotrix', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'purrr', 'nloptr', 'osqp', 'Rcpp', 'furrr'

Packages suggested but not available for checking:
  'covr', 'testthat', 'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ppcor', 'crayon', 'ggcorrplot', 'glue', 'psych', 'clipr',
  'tidyselect', 'moments', 'ggpubr', 'ggplot2', 'magrittr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nloptr', 'msm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'genalg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cosinor', 'cowplot', 'scales', 'magrittr', 'stringr', 'purrr',
  'ggplot2', 'matrixStats', 'Hmisc'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'shiny'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
D.M: no visible global function definition for 'integrate'
lookbackTime: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'data.table', 'nloptr', 'MBA', 'mAr', 'matrixcalc',
  'mvtnorm', 'plotly', 'cowplot', 'directlabels', 'animation', 'pracma'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quadprog', 'Rglpk', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'wavethresh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'copula', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pracma', 'fdrtool'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'OpenMx', 'ctsem', 'lavaan', 'foreach', 'MBESS', 'crayon', 'psych',
  'doParallel', 'rootSolve', 'abind', 'RPushbullet', 'openxlsx',
  'zcurve', 'scholar', 'stringi'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tram', 'mlt', 'variables', 'basefun'

Packages suggested but not available for checking:
  'TH.data', 'knitr', 'colorspace', 'multcomp'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/cotram.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', 'bitops', 'httr', 'rjson'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'colordistance', 'png', 'jpeg'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scatterplot3d'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'quantreg', 'Hmisc', 'foreach', 'doRNG', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'shiny', 'pscl'

Packages suggested but not available for checking:
  'dplyr', 'DT', 'gridExtra', 'knitr', 'pander', 'reshape2',
  'rmarkdown', 'shinythemes', 'shinycssloaders', 'shinyWidgets',
  'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'msme', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'flexsurv', 'Formula', 'VGAM', 'optimx', 'numDeriv', 'car',
  'Rdpack', 'RColorBrewer', 'dplyr', 'standardize', 'pscl', 'lmtest',
  'xtable', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tibble', 'utf8'
Note: found 128392 marked UTF-8 strings
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:
  'Formula', 'expm', 'numDeriv', 'lmtest'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ComplexHeatmap', 'circlize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Biobase', 'limma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dataRetrieval', 'dplyr', 'ggplot2', 'lubridate', 'maps', 'plyr',
  'R.utils', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'hurricaneexposure', 'scales'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'lubridate'

Packages suggested but not available for checking:
  'choroplethr', 'choroplethrMaps', 'ggplot2', 'knitr', 'purrr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bio3d', 'matrixcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'TMB', 'rjags', 'inline', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixcalc', 'lubridate', 'zoo', 'gstat', 'sp', 'spacetime'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CholWishart'

Packages suggested but not available for checking:
  'knitr', 'plyr', 'spcov', 'qgraph', 'igraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'colourpicker', 'dplyr', 'egg', 'ggplot2', 'markdown',
  'shiny', 'shinyjs', 'tidyr', 'table1'

Packages suggested but not available for checking:
  'clipr', 'formatR', 'knitr', 'rmarkdown', 'mrgsolve', 'ggridges',
  'ggrepel', 'ggstance', 'patchwork', 'bayestestR', 'plotly', 'scales',
  'shinyAce', 'Rcpp', 'gamlss.dist'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RMTstat', 'corpcor'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tokenizers'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'mixggm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'ape', 'rentrez', 'plotly', 'htmlwidgets', 'deSolve',
  'gplots', 'pheatmap', 'shiny', 'shinydashboard', 'shinycssloaders',
  'DT', 'dplyr', 'collapsibleTree'

Packages suggested but not available for checking:
  'knitr', 'devtools', 'roxygen2', 'markdown', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'httr', 'lubridate', 'rio', 'rlang', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'data.tree', 'DT', 'networkD3'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'dplyr', 'glue', 'lubridate', 'magrittr', 'readr', 'stringr', '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: 'devtools'

Packages suggested but not available for checking:
  'remotes', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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', 'purrr', 'dplyr', 'readr', 'jsonlite', 'log4r', 'rJava',
  'tabulizer', 'modules', 'stringr', 'rvest', 'xml2', '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', 'lubridate', 'magrittr', 'mapview', 'plotly',
  'sf'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'dplyr', 'glue', 'httr', 'lubridate', 'magrittr', 'purrr',
  'snakecase', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'survey', 'readr', 'dplyr', 'magrittr', 'projmgr', 'httr', 'RCurl',
  'timeDate', 'readxl', 'tibble'

Packages suggested but not available for checking: 'tidyverse', 'convey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* DONE
Status: 1 ERROR
IPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'seqinr', 'stringr', 'ggpubr', 'dplyr',
  'VennDiagram'

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:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'stringi', 'devtools', 'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'covidsymptom-Ex.R' failed
The error most likely occurred in:

> ### Name: get_latest_data
> ### Title: Retrieve updated COVID Symptom Study Sweden (CSSS) data
> ### Aliases: get_latest_data
> 
> ### ** Examples
> 
> df <- get_latest_data(data_level = "county")
Error in loadNamespace(x) : there is no package called 'stringi'
Calls: get_latest_data ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'mlogit', 'poLCA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
covreg.mcmc: no visible global function definition for 'model.frame'
covreg.mcmc: no visible global function definition for 'model.matrix'
covreg.mcmc: no visible global function definition for 'model.response'
covreg.mcmc: no visible global function definition for 'lm'
covreg.mcmc: no visible global function definition for 'rnorm'
covreg.mcmc: no visible global function definition for 'cov'
rmn: no visible global function definition for 'rnorm'
rwish: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'digest', 'jsonlite', 'rex', 'httr', 'crayon', 'withr', 'yaml'

Packages suggested but not available for checking:
  'R6', 'curl', 'knitr', 'rmarkdown', 'htmltools', 'DT', 'testthat',
  'rlang', 'rstudioapi', 'xml2', 'memoise', 'mockery'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bnlearn', 'bindata', 'Matching', 'doRNG', 'glmnet', 'randomForest',
  'foreach', 'xtable', 'doParallel', 'bartMachine', 'tmle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dr', 'np'

Package suggested but not available for checking: 'bindata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvinecopulib', 'lavaan', 'nleqslv', 'PearsonDS', 'Rcpp', 'gsl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'purrr', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'geigen', 'shapes', 'expm', 'mvtnorm', 'doParallel',
  'foreach', 'pracma', 'Rdpack', 'SHT', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rgl', 'misc3d'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gtable', 'rlang', 'scales'

Packages suggested but not available for checking:
  'Cairo', 'covr', 'dplyr', 'forcats', 'gridGraphics', 'knitr',
  'magick', 'maps', 'PASWR', 'patchwork', 'rmarkdown', 'ragg',
  'testthat', 'tidyr', 'vdiffr', 'VennDiagram'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crayon', 'fortunes', 'rmsfact'

Packages suggested but not available for checking:
  'curl', 'jsonlite', 'knitr', 'multicolor', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rms', 'PermAlgo', 'dplyr', 'tidyr', 'ggplot2', 'gridExtra',
  'mediation'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bindrcpp'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'timereg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'nloptr', 'matrixcalc', 'SNPRelate', 'rARPACK', 'coxme',
  'microbenchmark', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bdsmatrix'

Packages suggested but not available for checking: 'mvtnorm', 'kinship2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for 'model.extract'
coxr: no visible global function definition for 'model.matrix'
coxr.draw: no visible global function definition for 'lines'
coxr.draw: no visible global function definition for 'points'
coxr.fit: no visible global function definition for 'quantile'
gen_data: no visible global function definition for 'rnorm'
gen_data: no visible global function definition for 'rexp'
plot.coxr: no visible global function definition for 'quantile'
plot.coxr: no visible global function definition for 'par'
plot.coxr: no visible global function definition for 'mtext'
plot.coxr: no visible global function definition for 'title'
plot.coxr: no visible global function definition for 'split.screen'
plot.coxr: no visible global function definition for 'screen'
plot.coxr: no visible global function definition for 'close.screen'
print.coxr: no visible global function definition for 'pnorm'
print.coxr: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq pnorm
  points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'BB', 'inline', 'gss', 'ggplot2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MESS', 'multtest', 'qvalue', 'limma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available:
  'Rdpack', 'Rcpp', 'purrr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'cointReg', 'foreach', 'doRNG', 'doParallel', 'ggplot2', 'dplyr',
  'tikzDevice', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forestplot', 'purrr', 'mvtnorm'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'abind', 'plyr'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running examples in 'cpca-Ex.R' failed
The error most likely occurred in:

> ### Name: cpc
> ### Title: Function cpc.
> ### Aliases: cpc
> 
> ### ** Examples
> 
> require(plyr)
Loading required package: plyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'plyr'
> require(abind)
Loading required package: abind
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'abind'
> 
> data(iris)
> 
> C <- daply(iris, "Species", function(x) cov(x[, -ncol(x)]))
Error in daply(iris, "Species", function(x) cov(x[, -ncol(x)])) : 
  could not find function "daply"
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fAsianOptions', 'Rdpack'

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 suggested but not available for checking: 'qvalue'
Package required but not available: 'matrixStats'

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/cplexAPI/cplexAPI.Rcheck/00install.out' for details.
Packages required but not available:
  'coda', 'biglm', 'ggplot2', 'minqa', 'reshape2', 'statmod', 'tweedie'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'plyr', 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'bench', 'brio', 'callr', 'cli', 'covr', 'decor', 'desc', 'ggplot2',
  'glue', 'knitr', 'lobstr', 'mockery', 'progress', 'rmarkdown',
  'scales', 'testthat', 'tibble', 'vctrs', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'
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 brio, cli, decor, desc, glue, tibble, vctrs package(s) are required for this functionality
Execution halted
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: 'ineq', 'kappalab', 'mc2d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'RcppProgress', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'igraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'nortest', 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'prodlim', 'tpr', 'geepack', 'lgtdl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lazyeval', 'lme4', 'magrittr', 'plot3D', 'Rcpp',
  'rgl', 'tibble', 'tidyr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'geepack', 'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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
Packages required but not available:
  'Rcpp', 'magrittr', 'mvtnorm', 'Rfast', 'tibble', 'dplyr', 'tidyr',
  'rlang', 'ggplot2', 'gridExtra', 'RcppArmadillo'

Package suggested but not available for checking: 'L1pack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'muhaz'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'Hmisc', 'knitr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'readr', 'dplyr', 'stringr', 'forcats', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'survey', 'srvyr', 'here', 'scales', 'ggplot2',
  'usmap'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', '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: 'magrittr', 'rvest', 'xml2'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randomForest', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'httr', 'jsonlite', 'anytime', 'snakecase', 'rlang', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'tibble', 'knitr', 'rmarkdown', 'leaflet',
  'scales', 'htmltools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'quantreg', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
distance.comoving: no visible global function definition for
  'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Package required but not available: 'expm'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'rvest', 'stringr', 'dplyr', 'igraph', 'Rcpp',
  'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking:
  'ggplot2', 'tibble', 'visNetwork', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DBI', 'debugme', 'desc', 'RSQLite'

Packages suggested but not available for checking:
  'covr', 'mockery', 'testthat', 'withr', 'zip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'visNetwork', 'colorspace', 'igraph', 'magrittr', 'stringr',
  'ggplot2', 'countrycode', 'wordcloud', 'tm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'curl', 'shiny', 'shinyjs', 'miniUI', 'stringr', 'DT',
  'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
crantastic.submitInstalledPackages: no visible global function
  definition for 'installed.packages'
postData: no visible global function definition for 'make.socket'
postData: no visible global function definition for 'write.socket'
postData: no visible global function definition for 'read.socket'
postData: no visible global function definition for 'close.socket'
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
Package required but not available: 'svMisc'

Packages suggested but not available for checking: 'NMF', 'recommenderlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'Rcpp', 'shiny', 'dplyr', 'raster', 'gdistance',
  'rmapshaper', 'sp', 'sf', 'magrittr', 'lubridate', 'tibble', 'purrr',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'rgdal', 'argosfilter', 'tidyr', 'xts', 'broom',
  'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mockery', 'rstudioapi', 'testthat', 'withr'
'LazyData' is specified without a 'data' directory
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
Packages required but not available:
  'Formula', 'ordinal', 'sandwich', 'scoringRules'

Packages suggested but not available for checking:
  'glmx', 'lmtest', 'memisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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:
  'openssl', 'sys', 'curl', 'jsonlite', 'askpass'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
cm.CVaR: no visible global function definition for 'quantile'
cm.hist: no visible global function definition for 'hist'
cm.quantile: no visible global function definition for 'qnorm'
cm.rnorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'data.table', 'dplyr', 'ggplot2', 'foreach', 'doParallel', 'glmnet',
  'cli', 'xgboost'

Packages suggested but not available for checking:
  'pdp', 'pmml', 'XML', 'knitr', 'gbm', 'randomForest', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fOptions'

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: 'ff', 'R.rsp', 'shiny'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'sandwich', 'survey', 'lmtest', 'ggplot2', 'ggstance', 'scales'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'httr', 'RSQLite', 'UpSetR', 'VennDiagram', 'ggplot2',
  'ggridges', 'R.utils', 'igraph'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'readxl', 'AnnotationDbi',
  'org.Hs.eg.db', 'clusterProfiler'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Rglpk'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'Rcpp', 'data.table'

Packages suggested but not available for checking:
  'udpipe', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'plotrix', 'ggplot2', 'scatterplot3d', 'forecast',
  'lubridate', 'XML', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'httr', 'magrittr', 'purrr', 'readr', 'stringr', 'tibble',
  'dplyr', 'sf'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'geosphere'

Packages suggested but not available for checking: 'fields', 'knitr', 'gbm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'gridExtra', 'scales', 'magrittr', 'gt',
  'tidyr', 'rlang'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Biostrings', 'gbm', 'GenomicRanges', 'BiocGenerics', 'IRanges',
  'GenomeInfoDb', 'S4Vectors', 'rtracklayer', 'stringr', 'vtreat',
  'shiny', 'DT'

Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'R6'

Packages suggested but not available for checking:
  'DiagrammeR', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DiagrammeR', 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'xml2', 'pdftools', 'hoardr'

Packages suggested but not available for checking:
  'roxygen2', 'rcrossref', 'testthat', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pcaMethods', 'Biobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridExtra', 'GenSA', 'mvtnorm', 'rjags'

Packages suggested but not available for checking:
  'ggmcmc', 'knitr', 'Rcpp', 'RcppArmadillo'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/crmPack-jss-paper.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FNN', 'ggplot2', 'gplots', 'pcaPP', 'plyr', 'robustbase', 'rrcov'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'chron', 'RCurl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'tinytest', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'shiny', 'shinydashboard', 'stringr', 'httr', 'dplyr', 'DT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/tutorial01.Rnw'
   'inst/doc/tutorial02.Rnw'
   'inst/doc/tutorial03.Rnw'
   'inst/doc/tutorial04.Rnw'
   'inst/doc/tutorial05.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/tutorial01.Rnw'
   'vignettes/tutorial02.Rnw'
   'vignettes/tutorial03.Rnw'
   'vignettes/tutorial04.Rnw'
   'vignettes/tutorial05.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'htmltools', 'glue'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'shiny'
Note: found 3 marked UTF-8 strings
Packages required but not available:
  'dplyr', 'ggplot2', 'raster', 'rgdal', 'tidyr', 'ncdf4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'imager', 'reshape2', 'EBImage'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'raster', 'sf', 'data.table', 'httr', 'RJSONIO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'tidyr', 'ggplot2', 'rgdal', 'ncdf4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'AlgDesign', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'broom', 'dplyr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'covr', 'crayon', 'furrr', 'future', 'testthat', 'tibble', 'withr'

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:
  'ggplot2', 'crossdes', 'xtable', 'rJava', 'CommonJavaJars', 'Rcpp',
  'RcppArmadillo', 'JavaGD', 'multcomp', 'digest'

Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Crossover.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BootC : BSs: no visible global function definition for 'lm'
BootC : BSs: no visible global function definition for 'vcov'
BootC: no visible global function definition for 'boot'
BootC: no visible global function definition for 'boot.ci'
DeltaC: no visible global function definition for 'lm'
DeltaC: no visible global function definition for 'vcov'
FiellerC: no visible global function definition for 'lm'
FiellerC: no visible global function definition for 'vcov'
nonLinearC: no visible global function definition for 'nls'
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Package required but not available: 'Rmpfr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'dplyr', 'ellipsis', 'flextable', 'forcats', 'glue',
  'lifecycle', 'nortest', 'officer', 'purrr', 'rlang', 'stringr',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'covr', 'crayon', 'xml2', 'DescTools', 'digest', 'gt', 'expss',
  'ggplot2', 'gmodels', 'Hmisc', 'jsonlite', 'knitr', 'openxlsx',
  'rmarkdown', 'sloop', 'stringi', 'systemfonts', 'testthat', 'withr',
  'waldo'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'jsonlite', 'lazyeval', 'R6'

Packages suggested but not available for checking:
  'shiny', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Modeler', 'oompaBase'

Package suggested but not available for checking: 'Biobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'sda', 'care', 'binda'
Package required but not available: 'stringi'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'openVA'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'haven', 'labelled', 'readr', 'readxl', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'dplyr', 'stringr', 'magrittr', 'jsonlite', 'r6extended'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'VGAM', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'randomcoloR', 'lucid', 'dplyr', 'png'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crunch', 'dplyr', 'ggplot2', 'httptest', 'lazyeval', 'lifecycle',
  'purrr', 'tibble', 'rlang', 'scales', 'stringr', 'tidyselect',
  'viridisLite'

Packages suggested but not available for checking:
  'covr', 'magrittr', 'spelling', 'vdiffr', 'knitr', 'testthat',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pracma', 'tseriesChaos', 'gplots', 'plot3D', 'FSA', 'rdist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cmprsk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
crrc: no visible binding for global variable 'na.omit'
crrs: no visible binding for global variable 'na.omit'
mycrr: no visible binding for global variable 'na.omit'
mycrr.test: no visible binding for global variable 'na.omit'
print.crrs: no visible global function definition for 'pnorm'
psh.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
Package required but not available: 'cmprsk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sandwich'

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', 'spelling'
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: 'foreach'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'readr', 'digest', 'tidytext', 'tibble',
  'rcorpora', 'knitr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'np', 'quantreg'

Packages suggested but not available for checking:
  'logspline', 'quadprog', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'plyr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'e1071', 'randomForest', 'adabag', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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.
Packages required but not available:
  'curl', 'R6', 'urltools', 'httpcode', 'jsonlite', 'mime'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'fauxpas', 'webmockr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'crayon', 'curl', 'httr', 'httpcache', 'jsonlite'

Packages suggested but not available for checking:
  'covr', 'crunchy', 'devtools', 'haven', 'httptest', 'keyring',
  'knitr', 'lintr', 'magrittr', 'rmarkdown', 'rstudioapi', 'spelling',
  'styler', 'testthat', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crunch', 'shiny', 'httpcache', 'miniUI', 'rstudioapi'

Packages suggested but not available for checking:
  'covr', 'htmltools', 'httptest', 'knitr', 'rmarkdown', 'shinytest',
  'spelling', 'testthat', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'raster', 'stringr', 'lubridate', 'ncdf4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'DT', 'geosphere', 'mapdata', 'marmap', 'maps', 'shiny',
  'shinydashboard', 'shinyjs', 'stringr', 'swfscDAS'

Packages suggested but not available for checking: 'httr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rJPSGCS', 'car', 'ellipse', 'chopsticks'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'flux', 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'BMisc', 'pbapply', 'progress', 'qte'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'marg', 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'data.table', 'scales', 'reshape2', 'moments', 'Lmoments',
  'foreach', 'ggpubr', 'raster', 'doParallel'

Packages suggested but not available for checking: 'testthat', 'colorspace'

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.
Packages required but not available:
  'lpSolve', 'mcclust', 'moments', 'DNAcopy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'alabama', 'cli', 'crayon', 'expm', 'future.apply',
  'future', 'lavaan', 'magrittr', 'matrixcalc', 'matrixStats',
  'polycor', 'progressr', 'psych', 'purrr', 'Rdpack', 'rlang',
  'symmoments', 'lifecycle'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'knitr', 'nnls', 'prettydoc', 'plotly',
  'rmarkdown', 'rootSolve', 'listviewer', 'testthat', 'ggplot2',
  'openxlsx'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'NLP', 'tm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Biostrings'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fabia', 'pls', 'FactoMineR', 'elasticnet', 'randomcoloR', 'snowFT'

Packages suggested but not available for checking:
  'knitr', 'gplots', 'viridis'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/CSFA.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fuzzyjoin', 'purrr', 'httr', 'stringr', 'jsonlite', 'magrittr',
  'dplyr', 'extrafont', 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sp', 'maptools', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mco', 'ROCR', 'zoo', 'caTools', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'httr', 'jsonlite', 'reshape2', 'rjstat', 'R.cache', 'sf'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tmap', 'viridisLite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'stringr', 'readr', 'tidyselect', 'ggplot2', 'mapproj',
  'rlang', 'haven', 'purrr', 'csppData'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggraph', 'igraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'compiler'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable 'quantile'
csSAM: no visible global function definition for 'median'
csfit: no visible global function definition for 'lsfit'
csfit: no visible global function definition for 'ls.diag'
plotCsSAM: no visible global function definition for 'pdf'
plotCsSAM: no visible global function definition for 'par'
plotCsSAM: no visible global function definition for 'title'
plotCsSAM: no visible global function definition for 'dev.off'
runSAM: no visible binding for global variable 'median'
runSAM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
Package required but not available: 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'fastcluster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
cstar: no visible global function definition for 'vcov'
cstar : utility: no visible global function definition for 'dt'
cstar : maximand: no visible global function definition for 'integrate'
cstar: no visible global function definition for 'uniroot'
cstari : utility: no visible global function definition for 'dt'
cstari : maximand: no visible global function definition for
  'integrate'
cstari: no visible global function definition for 'uniroot'
cstarme : utility: no visible global function definition for 'density'
cstarme : maximand: no visible global function definition for
  'integrate'
cstarme : maximand: no visible global function definition for 'sd'
cstarme: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
Packages required but not available:
  'maps', 'qmap', 'easyVerification', 's2dverification', 's2dv',
  'rainfarmr', 'multiApply', 'ClimProjDiags', 'ncdf4', 'plyr', 'abind',
  'data.table', 'reshape2', 'ggplot2', 'RColorBrewer', 'verification'

Packages suggested but not available for checking:
  'zeallot', 'testthat', 'knitr', 'markdown', 'rmarkdown', 'startR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'relaxo', 'caret', 'futile.logger', 'glmnet', 'ncvreg',
  'shiny', 'shinyjs', 'DT', 'HDCI', 'reshape2', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'bit64'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'data.table', 'jsonlite', 'yaml'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyMatrix', 'epitools', 'rpivotTable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gmp', 'igraph'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'huge', 'ggplot2', 'gplots', 'RColorBrewer',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mirt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qtl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'coda', 'expm', 'numDeriv', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp', 'markovchain'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'fda', 'gdistance', 'sp'

Packages suggested but not available for checking: 'dismo', 'crawl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SuperLearner', 'tmle', 'glmnet'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Bessel', 'data.table', 'digest', 'expm', 'fasttime', 'Gmedian',
  'gsl', 'manipulate', 'numDeriv', 'pbivnorm', 'pracma', 'raster',
  'rgdal', 'shape', 'sp', 'statmod'

Packages suggested but not available for checking:
  'bit64', 'fftw', 'knitr', 'move', 'rmarkdown', 'suncalc'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jiebaR', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clinfun', 'diagram', 'emmeans', 'dplyr', 'magrittr', 'shape',
  'Gmisc'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pch'

Packages suggested but not available for checking: 'car', 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'httr', 'curl', 'clipr', 'xml2', 'rvest', 'nodbi', 'DBI',
  'stringi'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'RSQLite', 'mongolite', 'tinytest',
  'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ctsem', 'OpenMx', 'plyr'

Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/ctsem.rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'cOde', 'expm', 'data.table', 'Deriv', 'ggplot2', 'mize',
  'mvtnorm', 'pkgbuild', 'plyr', 'rstan', 'RcppParallel', 'tibble',
  'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'devtools', 'DEoptim', 'tinytex', 'lme4',
  'shiny', 'gridExtra', 'arules'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/hierarchicalmanual.rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable',
  'rpart.plot', 'party'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable',
  'rpart.plot', 'party'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CTT', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyAce', 'CTT', 'ltm', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'XML'
Running examples in 'ctv-Ex.R' failed
The error most likely occurred in:

> ### Name: ctv-server
> ### Title: CRAN Task Views: Tools for Maintainers
> ### Aliases: read.ctv ctv2html check_ctv_packages repos_update_views
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## read .ctv file
> x <- read.ctv(system.file("ctv", "Econometrics.ctv", package = "ctv"))
Error in loadNamespace(x) : there is no package called 'XML'
Calls: read.ctv ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'read-all.R'
Running the tests in 'tests/read-all.R' failed.
Last 13 lines of output:
  [31] "Spatial.ctv"                   "SpatioTemporal.ctv"           
  [33] "Survival.ctv"                  "TimeSeries.ctv"               
  [35] "WebTechnologies.ctv"           "gR.ctv"                       
  > 
  > rr <- sapply(ctvs,
  + 	     function(ctv) {
  + 		 cat(sprintf("%25s  ",ctv))
  + 		 R <- read.ctv(file.path(cdir, ctv))
  + 		 cat("[ok]\n")
  +                  R
  + 	     },
  + 	     simplify=FALSE)
               Bayesian.ctv  Error in loadNamespace(x) : there is no package called 'XML'
  Calls: sapply ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Errors in running code in vignettes:
when running code in 'ctv-howto.Rnw'
  ...

> library("ctv")

> x <- read.ctv(system.file("ctv", "Econometrics.ctv", 
+     package = "ctv"))

  When sourcing 'ctv-howto.R':
Error: there is no package called 'XML'
Execution halted

  'ctv-howto.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'ctv-howto.Rnw' using Sweave

Error: processing vignette 'ctv-howto.Rnw' failed with diagnostics:
 chunk 1 
Error in loadNamespace(x) : there is no package called 'XML'

--- failed re-building 'ctv-howto.Rnw'

SUMMARY: processing the following file failed:
  'ctv-howto.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'mvtnorm', 'benchr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'glue', 'pillar', 'purrr', 'rlang', 'tibble', 'tidyselect'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'htmltools', 'htmlwidgets', 'raster', 'stars',
  'viridisLite'

Package suggested but not available for checking: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'foreach'

Packages suggested but not available for checking:
  'seqinr', 'VGAM', 'EMCluster'

Package which this enhances but not available for checking: 'pbdMPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'reshape2'

Packages suggested but not available for checking:
  'mlbench', 'caret', 'knitr', 'modeldata', 'dplyr', 'rlang',
  'tidyrules'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Formula'

Packages suggested but not available for checking: 'knitr', 'digest'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/CUBvignette-knitr.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xlsx', 'xtable', 'DT', 'lmerTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'combinat', 'Hmisc', 'pspearman', 'stringi'

Packages suggested but not available for checking:
  'memoise', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
Package required but not available: 'lars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'magrittr', 'readr', 'rlang', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'rstpm2', 'date', 'numDeriv', 'statmod', 'relsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'spelling', 'testthat', 'knitr', 'jsonlite', 'rmarkdown', 'magrittr',
  'httpuv', 'webutils'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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 examples in 'curl-Ex.R' failed
The error most likely occurred in:

> ### Name: curl_echo
> ### Title: Echo Service
> ### Aliases: curl_echo
> 
> ### ** Examples
> 
> h <- new_handle(url = 'https://httpbin.org/post')
> handle_setform(h, foo = "blabla", bar = charToRaw("test"),
+   myfile = form_file(system.file("DESCRIPTION"), "text/description"))
> 
> # Echo the POST request data
> formdata <- curl_echo(h)
Error in loadNamespace(x) : there is no package called 'httpuv'
Calls: curl_echo ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
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
Package required but not available: 'cmprsk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'keypress'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'multcomp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ddalpha', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'feature', 'geometry', 'hdrcde', 'ks', 'misc3d', 'ptinpoly', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plot3D'
Error(s) in re-building vignettes:
--- re-building 'Cusp-JSS.Rnw' using Sweave
--- finished re-building 'Cusp-JSS.Rnw'

--- re-building 'cusp-hands-on-examples.Rnw' using Sweave
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Warning in model.matrix.default(mta, mfa, contrasts) :
  non-list contrasts argument ignored
Warning in model.matrix.default(mtb, mfb, contrasts) :
  non-list contrasts argument ignored
Loading required package: plot3D
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'plot3D'
Loading required package: plot3D
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'plot3D'
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "cusp-hands-on-examples.tex" --max-iterations=20 -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/tex/latex" -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'cusp-hands-on-examples.Rnw' failed with diagnostics:
running 'texi2dvi' on 'cusp-hands-on-examples.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex (file ./cusp-hands-on-examples-fig1.pdf): PDF inclusion
: required page does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!

--- failed re-building 'cusp-hands-on-examples.Rnw'

SUMMARY: processing the following file failed:
  'cusp-hands-on-examples.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'FNN', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'dplyr', 'tibble', 'magrittr', 'purrr', 'tidyselect',
  'generics', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'checkmate', 'data.table', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'rmarkdown'

Packages which this enhances but not available for checking:
  'vdiffr', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'set', 'do', 'ROCit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gridExtra', 'foreach', 'dplyr', 'tidyselect', 'tidyr', 'purrr',
  'tibble', 'ggplot2', 'Rcpp', 'rlang'

Packages suggested but not available for checking:
  'fANCOVA', 'testthat', 'doRNG', 'doParallel', 'knitr', 'rmarkdown',
  'crayon', 'registry', 'pkgmaker', 'vctrs'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
delta.glm: no visible global function definition for 'glm'
delta.glm: no visible global function definition for 'residuals'
delta.glm: no visible global function definition for 'fitted'
delta.glm: no visible global function definition for 'predict.glm'
two.stage.model.outputs: no visible global function definition for 'sd'
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
Package required but not available: 'mda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gbutils', 'Rdpack', 'fGarch'

Packages suggested but not available for checking:
  'testthat', 'PerformanceAnalytics', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ROCR', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
calfun: no visible global function definition for 'optim'
calfun: no visible global function definition for 'cov'
calfun: no visible global function definition for 'var'
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
Packages required but not available:
  'matrixStats', 'origami', 'coop', 'Rdpack', 'rlang', 'dplyr',
  'stringr', 'purrr', 'tibble', 'assertthat', 'RSpectra', 'ggplot2',
  'ggpubr', 'RColorBrewer'

Packages suggested but not available for checking:
  'future', 'future.apply', 'testthat', 'knitr', 'rmarkdown', 'covr',
  'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'R6', 'SciViews', 'MBESS'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tableone'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'png', 'gWidgets2', 'RGtk2'
Package required but not available: 'limSolve'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'ggrepel'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'rmarkdown', 'testthat', 'dplyr', 'tidyr',
  'ggbeeswarm', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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
Skipping vignette re-building
Packages suggested but not available for checking:
  'geepack', 'knitr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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
Packages required but not available:
  'doParallel', 'foreach', 'ggplot2', 'dplyr', 'glasso'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CompQuadForm'

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', 'checkmate', 'data.table', 'dplyr',
  'ggplot2', 'lifecycle', 'lme4', 'MuMIn', 'plyr', 'pROC', 'purrr',
  'recipes', 'rlang', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'AUC', 'covr', 'e1071', 'furrr', 'ggimage', 'ggnewscale',
  'groupdata2', 'knitr', 'randomForest', 'rmarkdown', 'rsvg',
  'testthat', 'xpectr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
func.constructRegressionFormula: no visible global function definition
  for 'as.formula'
func.crossValidationAnalysis: no visible global function definition for
  'glm'
func.crossValidationAnalysis: no visible global function definition for
  'predict'
func.crossValidationAnalysis: no visible global function definition for
  'write.table'
func.externalValidationAnalysis: no visible global function definition
  for 'predict'
func.externalValidationAnalysis: no visible global function definition
  for 'write.table'
func.linearRegressionAnalysis: no visible global function definition
  for 'glm'
func.linearRegressionAnalysis: no visible global function definition
  for 'predict'
func.linearRegressionAnalysis: no visible global function definition
  for 'write.table'
func.sortDataColumns: no visible global function definition for
  'write.table'
mainfunc.q2: no visible global function definition for 'write.table'
mainfunc.q2: no visible global function definition for 'new'
mainfunc.stats: no visible global function definition for 'write.table'
mainfunc.stats: no visible global function definition for 'new'
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking:
  'testthat', 'covr', 'tibble'
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: 'PMA', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kernlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'wavethresh', 'EbayesThresh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
random.CV: no visible global function definition for 'var'
regular.CV: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Packages required but not available:
  'R6', 'Rcpp', 'bit64', 'gmp', 'Rmpfr', 'ECOSolveR', 'scs', 'osqp',
  'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'nnls', 'slam', 'covr'

Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc', 'cccp', 'Rmosek', 'Rglpk'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'R6', 'xml2', 'stringi', 'curl', 'RcppCWB', 'pbapply',
  'cli', 'jsonlite', 'httr', 'rstudioapi', 'zen4R'

Packages suggested but not available for checking:
  'tm', 'knitr', 'tokenizers', 'tidytext', 'SnowballC', 'janeaustenr',
  'NLP', 'testthat', 'rmarkdown', 'openNLP', 'aws.s3'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'matlab', 'permute'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'optimx', 'mvtnorm'

Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'dplyr', 'magrittr', 'knitr', 'stringr',
  'rmarkdown', 'testthat', 'BB', 'ucminf', 'dfoptim', 'minqa',
  'hydroPSO', 'GenSA', 'DEoptimR', 'nloptr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'inline'

Package suggested but not available for checking: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'xml2'

Packages suggested but not available for checking:
  'changepoint', 'minpack.lm', 'RCurl', 'raster', 'pspline', 'leaflet',
  'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'magrittr', 'jsonlite', 'httr', 'stringr', 'geodist'

Packages suggested but not available for checking: 'stplanr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'crayon', 'desc', 'remotes', 'withr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'flexsurv', 'lubridate', 'magrittr', 'mvtnorm', 'plyr', 'scales'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'Rcpp', 'Andromeda', 'dplyr', 'bit64', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'gnm', 'ggplot2', 'microbenchmark', 'cmprsk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringi', 'memoise', 'pingr'

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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'getPass', 'openssl', 'sodium'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'magrittr', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CytobankAPI', 'shiny', 'xlsx', 'shinyFiles', 'pheatmap'

Packages suggested but not available for checking:
  'httr', 'curl', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CytobankAPI'

Package suggested but not available for checking: 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GenKern', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'RColorBrewer'

Packages suggested but not available for checking:
  'dplyr', 'reshape2', 'bodenmiller', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'igraph', 'mclust', 'cowplot', 'GoFKernel',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'formatR', 'rmarkdown', 'viridis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'doParallel', 'dplyr', 'foreach', 'futile.logger',
  'magrittr', 'purrr', 'rlang', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'DBI', 'dbplyr', 'knitr', 'lazyeval', 'readr', 'rmarkdown',
  'RSQLite', 'stringr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'httr', 'readr', 'dplyr', 'magrittr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'scales', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'dplyr', 'httr', 'jsonlite', 'lifecycle', 'magrittr',
  'readr', 'rlang', 'stringi', 'stringr', '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: 'RSQLite', 'DBI'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'rjson', 'whisker'

Package suggested but not available for checking: 'RCurl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'magrittr', 'htmlwidgets', 'functional',
  'RColorBrewer', 'titanic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'htmltools', 'rlang', 'tidyr'

Packages suggested but not available for checking:
  'httr', 'jsonlite', 'listviewer', 'purrr', 'testthat'

Packages which this enhances but not available for checking:
  'igraph', 'partykit', 'treemap', 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'stringr', 'htmlwidgets', 'plyr', 'dplyr'

Packages suggested but not available for checking: 'shiny', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'limma'

Packages suggested but not available for checking:
  'DAAG', 'locfit', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/marray-notes.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'latticeExtra'

Packages suggested but not available for checking:
  'leaps', 'oz', 'lme4', 'quantreg', 'knitr', 'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/simulate-regdiags.Rnw'
   'inst/doc/simulate-varselect.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'magrittr', 'cowplot', 'dplyr', 'effsize', 'ellipsis', 'ggplot2',
  'forcats', 'ggforce', 'ggbeeswarm', 'plyr', 'RColorBrewer', 'rlang',
  'simpleboot', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tufte', 'testthat', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'knitr', 'RMariaDB'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'httr', 'beepr', 'curl', 'dplyr', 'png'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'e1071', 'DescTools'

Packages suggested but not available for checking:
  'multigroup', 'knitr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plyr'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FrF2', 'stringi'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'V8', 'jsonlite'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 's20x'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'V8', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'base64enc', 'testthat', 'markdown', 'rmarkdown', 'lavaan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
allCombs: no visible global function definition for 'combn'
brute.search: no visible global function definition for 'na.omit'
dag.draw: no visible global function definition for 'text'
dag.init: no visible global function definition for
  'installed.packages'
dag.legend: no visible global function definition for 'text'
dag.letter: no visible global function definition for 'text'
dag.move: no visible global function definition for 'identify'
dag.move: no visible global function definition for 'locator'
dag.sim: no visible global function definition for 'rnorm'
dag.sim: no visible global function definition for 'rbinom'
dag.sim : <anonymous>: no visible global function definition for
  'rbinom'
garrows: no visible global function definition for 'arrows'
smoothArc: no visible global function definition for 'points'
summary_dagRdag: no visible global function definition for 'na.omit'
viv: no visible global function definition for 'na.omit'
write.paths: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "points",
             "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'deSolve', 'DDD', 'subplex', 'tensor', 'pracma', 'testit', 'foreach',
  'doParallel', 'magrittr'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'gridExtra', 'dplyr',
  'ggplot2', 'ggtree', 'tidytree', 'tidyr', 'purrr', 'ape', 'phytools',
  'tibble'

Package which this enhances but not available for checking: 'doMC'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'relations', 'sets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'iBreakDown', 'ingredients'

Packages suggested but not available for checking:
  'gower', 'ranger', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DALEX', 'reticulate', 'ggplot2', 'gridExtra'

Packages suggested but not available for checking:
  'auditor', 'ingredients', 'gbm', 'ggrepel', 'h2o', 'iml', 'lime',
  'localModel', 'mlr', 'mlr3', 'randomForest', 'recipes', 'rmarkdown',
  'xgboost', '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', 'effects', 'rstan', 'gamlss', 'ggplot2', 'xtable',
  'optiscale', 'AICcmodavg', 'latticeExtra', 'coda', 'glue',
  'clarkeTest', 'haven', 'survey', 'janitor', 'tidyr', 'tidyselect',
  'tibble', 'magrittr', 'dplyr', 'rlang', 'jtools', 'DT'

Packages suggested but not available for checking:
  'carData', 'knitr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caper', 'ape', 'deSolve', 'matrixStats', 'expm', 'picante', 'DDD',
  '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:
  'ggplot2', 'reshape2', 'ellipse', 'dplyr', 'scales', 'stringr',
  'truncnorm', 'triangle', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'lintr', 'knitr', 'rmarkdown', 'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'behavr', 'data.table', 'readr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'ggetho', 'zeitgebr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crul', 'fauxpas', 'janitor', 'readxl'

Packages suggested but not available for checking:
  'ggplot2', 'maps', 'mapproj', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gplots', 'polycor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyCpp'

Packages suggested but not available for checking:
  'anytime', 'data.table', 'zoo', 'xts', 'TTR', 'quantmod', 'rtweet'

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 required but not available:
  'tibble', 'ggplot2', 'stringr', 'purrr', 'rlang', 'fpc', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'mlbench', 'dplyr',
  'magrittr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'readr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'purrr', 'dplyr', 'ggplot2',
  'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
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', 'lubridate', 'stringdist', 'stringr', 'tidyr', 'xesreadR',
  'rlang', 'bupaR', 'readr', 'edeaR', 'magrittr', 'purrr', 'glue',
  'miniUI', 'shiny'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vegan'

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:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'httr', 'gridExtra', 'gtable', 'ggplot2', 'plyr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'plyr', 'tidyr', 'stringr', 'ape', 'vegan',
  'SNPRelate', 'StAMPP', 'sp', 'PopGenReport', 'hierfstat',
  'robustbase', 'gridExtra', 'HardyWeinberg', 'foreach', 'dplyr',
  'crayon', 'devtools'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgl', 'doParallel', 'data.table', 'reshape2',
  'pca3d', 'dismo', 'pegas', 'directlabels', 'rgdal',
  'leaflet.minicharts', 'leaflet', 'rrBLUP', 'poppr', 'Rcpp', 'igraph',
  'qvalue', 'gdistance', 'seqinr', 'pheatmap', 'RColorBrewer',
  'gplots', 'vcfR', 'mmod', 'plotly', 'ggthemes', 'ggrepel', 'raster'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
drawAimSpot: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'par'
drawBoard: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'text'
drawHeatmap: no visible global function definition for 'heat.colors'
drawHeatmap: no visible global function definition for 'par'
drawHeatmap: no visible global function definition for 'image'
drawHeatmap: no visible global function definition for 'rect'
generalExpScores: no visible global function definition for 'fft'
simpleExpScores: no visible global function definition for 'mvfft'
simpleExpScores: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft heat.colors image mvfft par points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "points", "rect", "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
Package required but not available: 'Rook'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'htmltools'

Packages suggested but not available for checking:
  'testthat', 'lintr', 'knitr', 'rmarkdown', 'glue', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dash', 'dashHtmlComponents', 'jsonlite', 'plotly', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'dash', 'dashCoreComponents', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'dash', 'dashHtmlComponents', 'dashTable', 'jsonlite'
Packages required but not available:
  'dashHtmlComponents', 'dashCoreComponents', 'dashTable', 'R6',
  'fiery', 'routr', 'plotly', 'reqres', 'jsonlite', 'htmltools',
  'assertthat', 'digest', 'base64enc', 'mime', 'crayon', 'brotli'

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:
  'dash', 'dashHtmlComponents'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', 'deSolve', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'reshape2', 'jsonlite', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rJava'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rJava', 'SqlRender', 'stringr', 'rlang', 'DBI', 'urltools', 'bit64'

Packages suggested but not available for checking:
  'aws.s3', 'R.utils', 'withr', 'testthat', 'DBItest', 'knitr',
  'rmarkdown', 'RSQLite', 'ssh', 'Andromeda', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'deldir', 'GeneralizedUmatrix', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DataVisualizations', 'knitr', 'rmarkdown', 'plotrix', 'geometry',
  'sp', 'spdep', 'AdaptGauss', 'ABCanalysis', 'rgl', 'png',
  'ProjectionBasedClustering', 'parallelDist', 'pracma', 'dendextend'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xlsx', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'htmltools', 'summarytools', 'dplyr', 'rlang', 'DT',
  'magrittr', 'plotly', 'purrr', 'glue', 'formatR', 'RColorBrewer',
  'clipr', 'rstudioapi', 'lubridate', 'shinyWidgets', 'htmlwidgets',
  'fs', '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: 'data.table', 'dplyr'

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:
  'dplyr', 'knitr', 'stringi', 'markdown'

Packages suggested but not available for checking:
  'testthat', 'data.table', 'tibble', 'bit64', 'rmarkdown', 'titanic'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'shiny', 'miniUI', 'Hmisc', 'htmltools', 'haven',
  'jsonlite', 'tibble'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'anytime', 'dplyr', 'glue', 'httr', 'lubridate', 'purrr', 'stringr',
  'tidyr', 'tibble'

Packages suggested but not available for checking:
  'rstudioapi', 'testthat', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyBS', 'shinyjs', 'shinythemes', 'rhandsontable',
  'rstudioapi', 'htmltools', 'miniUI'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gWidgets2', 'RGtk2', 'gWidgets2RGtk2', 'digest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'reshape2', 'scales', 'ggplot2', 'gridExtra',
  'rmarkdown', 'networkD3'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'jsonlite', 'nycflights13'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'data.table', 'magrittr', 'openxlsx', 'dplyr', 'plyr',
  'tidyr', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'gdata'
Packages required but not available: 'caret', 'GA', 'Rcpp'

Packages suggested but not available for checking:
  'doParallel', 'foreach', 'testthat', 'diagram', 'knitr', 'rmarkdown',
  'pander', 'dplyr', 'tidyr', 'purrr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'dplyr', 'httr', 'magrittr', 'plyr', 'stringr', 'rlang'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'plyr', 'xlsx', 'rChoiceDialogs'

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', 'gridExtra', 'haven', 'htmltools', 'magrittr', 'pander',
  'rmarkdown', 'robustbase', 'stringi', 'whoami'

Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DBI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RJSONIO', 'XML', 'RCurl', 'base64', 'gsubfn', 'markdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'shiny', 'shinyWidgets', 'DT', 'data.table', 'readxl',
  'rio', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'validate'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doSNOW', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'httr', 'lubridate', 'readr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'XML', 'hash', 'httr', 'stringi', 'stringr', 'datapack', 'plyr',
  'parsedate', 'uuid', 'base64enc', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'digest', 'openssl', 'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'config', 'future', 'httr', 'iterators', 'jsonlite', 'jsonvalidate',
  'purrr', 'R6', 'R.utils', 'readr', 'rlist', 'stringr',
  'tableschema.r', 'urltools', 'V8'

Packages suggested but not available for checking:
  'covr', 'curl', 'data.table', 'DBI', 'devtools', 'foreach',
  'httptest', 'knitr', 'rmarkdown', 'RSQLite', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'knitr', 'rmarkdown', 'desc', 'yaml', 'purrr', 'roxygen2',
  'devtools', 'assertthat', 'stringr', 'futile.logger', 'rprojroot',
  'usethis', 'crayon'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'covr', 'data.tree'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'clipr', 'rstudioapi'

Packages suggested but not available for checking:
  'tibble', 'testthat', 'knitr', 'rmarkdown', 'covr', 'data.table'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lubridate', 'stringr', 'progress', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'pander', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'scales', 'foreach', 'doParallel', 'dplyr', 'reshape2',
  'data.table', 'zoo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
checkDataQuality: no visible binding for global variable 'quantile'
checkDataQuality: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  quantile write.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Packages required but not available:
  'cowplot', 'dplyr', 'emmeans', 'ggplot2', 'ggpubr', 'lme4',
  'lubridate', 'MultinomialCI', 'parallelMap', 'R.devices', 'reshape',
  'rlang', 'robustbase'

Packages suggested but not available for checking:
  'anytime', 'digest', 'DT', 'flexdashboard', 'htmltools', 'knitr',
  'patchwork', 'rmarkdown', 'rstudioapi', 'testthat', 'tibble',
  'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridExtra', 'haven', 'htmltools', 'magrittr', 'pander',
  'rmarkdown', 'robustbase', 'stringi', 'whoami'

Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggplot2'
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
Packages required but not available:
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  'sf', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'knitr'
Packages required but not available: 'httr', 'jsonlite', 'yaml'

Packages suggested but not available for checking:
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  'beanplot', 'doBy', 'insuranceData', 'rmarkdown', 'ggplot2',
  'modelwordcloud', 'withr', 'memoise', 'rex'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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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 suggested but not available for checking: 'xts'
Packages required but not available: 'shiny', 'miniUI', 'DT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'data.table'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'tibble', 'shiny', 'rhandsontable', 'dplyr', 'tidyr', 'ggplot2',
  'magrittr'

Packages suggested but not available for checking:
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  'listviewer', 'maps'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'lazyeval', 'R6', 'magrittr', 'tibble'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  '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: 'Rcpp', 'purrr', 'BH'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'styler', 'rmarkdown', 'lintr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'bit64', 'yaml'
Packages required but not available: 'R6', 'stringi'

Packages suggested but not available for checking:
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  'networkD3', 'jsonlite', 'treemap', 'party', 'partykit',
  'doParallel', 'foreach', 'htmlwidgets', 'DiagrammeR', 'mockery'

Package which this enhances but not available for checking: 'igraph'

VignetteBuilder packages required for checking but not installed:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'assertr', 'shiny.semantic', 'knitr', 'purrr', 'dplyr',
  'tidyr', 'R6', 'rlang', 'rmarkdown', 'htmltools', 'htmlwidgets',
  'tibble'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'sp', 'pracma', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'plyr', 'MBA', 'ggmap', 'plotrix', 'rworldmap', 'rgl', 'ABCanalysis',
  'choroplethr', 'dplyr', 'R6', 'parallelDist', 'knitr', 'rmarkdown',
  'vioplot', 'ggExtra', 'plotly', 'htmlwidgets', 'diptest', 'moments',
  'signal', 'DatabionicSwarm', 'ggrepel'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmltools', 'jsonify', 'shiny'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'chron', 'SASxport'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tinytest'
Packages required but not available: 'httr', 'jsonlite', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'babynames', 'dplyr', 'forcats', 'fueleconomy', 'gapminder',
  'ggplot2', 'Lahman', 'nasaweather', 'nycflights13', 'rlang',
  'tibble', 'tidyr', 'yaml'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
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
Packages required but not available:
  'data.table', 'Formula', 'magrittr', 'progress', 'aoos'

Packages suggested but not available for checking:
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  'testthat', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'odbc', 'dplyr', 'RSQLite'

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: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'labdsv', 'vegan', 'tree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'ibdreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'raster', 'httr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'rgeos', 'rgdal', 'ncdf4', 'knitr', 'rmarkdown',
  'covr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'
Malformed Description field: should contain one or more complete sentences.
dbEmpLikeGOF: no visible global function definition for 'runif'
dbEmpLikeGOF: no visible global function definition for 'var'
dbEmpLikeGOF: no visible global function definition for 'rnorm'
emplikeGOFinternal: no visible global function definition for 'var'
getCutoff: no visible binding for global variable 'unifCut'
getCutoff: no visible binding for global variable 'normCut'
getCutoff: no visible global function definition for 'lm'
getCutoff: no visible binding for global variable 'distEqCut'
getPval: no visible binding for global variable 'unifCut'
getPval: no visible binding for global variable 'normCut'
getPval: no visible global function definition for 'lm'
getPval: no visible binding for global variable 'distEqCut'
helperPval: no visible global function definition for 'lm'
returnCutoff: no visible global function definition for 'quantile'
testfun2: no visible global function definition for 'runif'
testfun2: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'dbEmpLikeGOF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'chk', 'flobr', 'glue', 'DBI', 'RSQLite', 'crayon', 'clisymbols',
  'rlang'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fdrtool'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'reshape2', 'XML'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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  'magrittr', 'rmarkdown', 'rprojroot', 'RMariaDB', 'RSQLite',
  'testthat', 'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'blob', 'hms'
Running examples in 'DBI-Ex.R' failed
The error most likely occurred in:

> ### Name: DBI-package
> ### Title: DBI: R Database Interface
> ### Aliases: DBI DBI-package
> 
> ### ** Examples
> 
> RSQLite::SQLite()
Error in loadNamespace(x) : there is no package called 'RSQLite'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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:
  'blob', 'callr', 'DBI', 'desc', 'hms', 'lubridate', 'R6', 'rlang',
  'testthat', 'withr'

Packages suggested but not available for checking:
  'debugme', 'devtools', 'knitr', 'lintr', 'rmarkdown', 'RSQLite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'xgboost', 'CatEncoders', 'Metrics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.core', 'spatstat.geom', 'Rcpp', 'ggplot2', 'cubature',
  'RcppParallel', 'reshape2', 'spatstat.utils', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'pkgdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bnlearn', 'bnviewer', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bnlearn', 'data.table', 'Rcpp', 'magrittr', 'R6'

Packages suggested but not available for checking: 'visNetwork', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'dplyr', 'odbc', 'progress', 'purrr', 'readr', 'RMariaDB',
  'RSQLite', 'tibble', 'XML'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rlang', 'ggplot2', 'purrr', 'magrittr'

Packages suggested but not available for checking:
  'dbplyr', 'testthat', 'tidyr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'blob', 'DBI', 'dplyr', 'ellipsis', 'glue',
  'lifecycle', 'magrittr', 'purrr', 'R6', 'rlang', 'tibble',
  'tidyselect', 'vctrs', 'withr'

Packages suggested but not available for checking:
  'bit64', 'covr', 'knitr', 'Lahman', 'nycflights13', 'odbc',
  'RMariaDB', 'rmarkdown', 'RPostgres', 'RPostgreSQL', 'RSQLite',
  'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'fpc', 'microbenchmark', 'testthat', 'dendextend', 'igraph', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package suggested but not available for checking: 'proxy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'data.table', 'stringi', 'html5'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DBI'

Packages suggested but not available for checking:
  'testthat', 'urltools', 'RSQLite', 'RMariaDB', 'RMySQL', 'RPostgres',
  'RPostgreSQL', 'hms', 'jsonlite', 'blob', 'odbc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'c3net', 'igraph', 'RedeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GPArotation', 'PMA', 'coin', 'elasticnet', 'locfdr', 'modeest',
  'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'checkmate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'interval', 'Formula'

Package suggested but not available for checking: 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'maxLik', 'rumidas', 'rugarch', 'roll', 'xts', 'tseries',
  'Rdpack', 'lubridate', 'zoo', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shinyBS', 'config', 'ggplot2', 'glue', 'golem', 'htmltools',
  'knitr', 'markdown', 'purrr', 'reactable', 'readr', 'readxl',
  'reticulate', 'rlang', 'shiny', 'shinydashboard', 'shinyjs', 'skimr',
  'tibble', 'visdat'

Packages suggested but not available for checking:
  'covr', 'jsonlite', 'jsonvalidate', 'rmarkdown', 'stringr',
  'testthat', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'data.table', 'igraph', 'ggplot2', 'ROCR', 'lsa', 'WGCNA',
  'qlcMatrix', 'foreach', 'plyr', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'matrixcalc', 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'limma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'dnet'

Packages suggested but not available for checking: 'foreach', 'doMC', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'devtools', 'png'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'xts', 'zoo', 'outliers', 'pracma', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'rjags', 'rstan'

Packages suggested but not available for checking:
  'R2WinBUGS', 'R2OpenBUGS', 'BRugs', 'rlecuyer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'spacetime', 'DCluster', 'xts', 'lme4'

Packages suggested but not available for checking:
  'INLA', 'pscl', 'RColorBrewer', 'gridExtra', 'latticeExtra'

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: 'openssl', 'phylogram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CDM'

Package suggested but not available for checking: 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dclone', 'coda'

Package suggested but not available for checking: 'rjags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'yaml', 'validate', 'settings'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'lumberjack'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'seqinr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doParallel', 'energy', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'beepr', 'dplyr', 'forcats',
  'janitor', 'purrr', 'tibble', 'tidyr', 'StanHeaders', 'BH',
  'RcppEigen'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'stackoverflow', 'mclust', 'ppcor', 'ggplot2', 'dplyr',
  'Rdpack'

Packages suggested but not available for checking: 'testthat', 'snow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'robustbase', 'sfsmisc', 'geometry', 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'ape', 'phytools', 'subplex', 'expm', 'SparseM'

Packages suggested but not available for checking: 'testthat', 'testit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ring'

Packages suggested but not available for checking:
  'deSolve', 'knitr', 'microbenchmark', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lokern', 'wavethresh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
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: 'segmented', 'qpdf'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'knitr', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'admisc', 'haven', 'readr', 'tibble', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dbscan', 'proxy', 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RSpectra', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'dplyr', 'ggplot2', 'lazyeval', 'magrittr', 'mixtools', 'plyr',
  'readr', 'shiny', 'shinyjs', 'tibble'

Packages suggested but not available for checking:
  'ggExtra', 'gridExtra', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggalt', 'MEGENA', 'igraph', 'Hmisc', 'plyr', 'scales',
  'VennDiagram'

Packages suggested but not available for checking:
  'WGCNA', 'Biostrings', 'impute', 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'irlba', 'Rcpp', 'RcppEigen', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'orthopolynom', 'evd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ifft: no visible global function definition for 'fft'
lines.deamer: no visible global function definition for 'lines'
rlaplace: no visible global function definition for 'runif'
Undefined global functions or variables:
  fft lines runif
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
Packages required but not available:
  'lpSolve', 'ggplot2', 'tidyr', 'plotly', 'igraph', 'writexl',
  'dplyr', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'aphid', 'seqinr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'truncdist', 'coda', 'RColorBrewer', 'mvtnorm', 'plyr',
  'PBSddesolve'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'devtools', 'R.rsp', 'beanplot'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crayon'

Packages suggested but not available for checking:
  'covr', 'mockery', 'R6', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rprojroot', 'rstudioapi'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ggplot2', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
compare.relimp: no visible global function definition for 'qchisq'
compare.relimp: no visible global function definition for 'pchisq'
plot_transition: no visible global function definition for 'dnorm'
plot_transition: no visible global function definition for 'par'
plot_transition: no visible global function definition for 'lines'
plot_transition: no visible global function definition for 'plogis'
plot_transition: no visible global function definition for 'axis'
plot_transition: no visible global function definition for 'mtext'
relative.importance: no visible global function definition for 'glm'
relative.importance: no visible global function definition for 'sd'
relative.importance : tr.pr: no visible global function definition for
  'pnorm'
relative.importance: no visible global function definition for 'vcov'
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis pnorm qchisq sd vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'oz', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'assertthat', 'chillR', 'dplyr', 'fANCOVA', 'ggplot2', 'ggstance',
  'magrittr', 'msm', 'mvtnorm', 'nleqslv', 'patchwork',
  'rriskDistributions', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'eha', 'knitr', 'mc2d', 'pls', 'rmarkdown', 'scales', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'htmltools', 'magrittr', 'base64enc', 'yaml',
  'jsonlite', 'readr', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'rprojroot', 'sf', 'scales',
  'RColorBrewer'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'randomizr', 'fabricatr', 'estimatr', 'rlang', 'generics'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'AER', 'diffobj', 'dplyr',
  'data.table', 'tibble', 'ggplot2', 'future.apply', 'broom',
  'Matching', 'betareg', 'biglm', 'gam', 'sf', 'reshape2',
  'DesignLibrary', 'coin', 'margins'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'DT', 'testthat', 'knitr', 'rmarkdown', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
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:
  'PSF', 'Rlibeemd', 'forecast', 'tseries'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'StratigrapheR', 'hht', 'hexbin', 'colorRamps', 'dplyr'

Packages suggested but not available for checking:
  'EMD', 'astrochron', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'gvc', 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
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
DeconCPdf: no visible global function definition for 'bw.nrd0'
DeconCPdf: no visible global function definition for 'bw.nrd'
DeconCPdf: no visible global function definition for 'bw.ucv'
DeconCPdf: no visible global function definition for 'bw.bcv'
DeconCPdf: no visible global function definition for 'bw.SJ'
DeconCPdf: no visible global function definition for 'density'
DeconCPdf: no visible global function definition for 'dnorm'
bw.dboot2 : suppL2: no visible global function definition for 'density'
bw.dboot2 : suppL2: no visible global function definition for 'rnorm'
bw.dboot2 : gaussL2: no visible global function definition for
  'density'
bw.dboot2 : gaussL2: no visible global function definition for 'rnorm'
bw.dmise: no visible global function definition for 'var'
plot.Decon: no visible global function definition for 'plot.default'
plot.Decon: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm plot.default
  rnorm var
Consider adding
  importFrom("graphics", "abline", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "rnorm", "var")
to your NAMESPACE file.
Packages required but not available:
  'reshape2', 'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19', 'GenomeInfoDb'

Package suggested but not available for checking: 'VariantAnnotation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'RWeka', 'RWekajars', 'rJava'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'purrr'

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', 'vctrs'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', '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', 'JGR', 'car', 'rJava', 'e1071', 'scales', 'plyr',
  'multcomp', 'effects'

Packages suggested but not available for checking:
  'lawstat', 'Hmisc', 'XLConnect'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'JavaGD', 'Deducer', 'sp', 'maptools', 'OpenStreetMap', 'scales',
  'rgdal', 'UScensus2010', 'Hmisc'

Package suggested but not available for checking: 'UScensus2010'

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.
Package required but not available: 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Deducer', 'tm', 'wordcloud', 'RColorBrewer', 'SnowballC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'editrules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lintools', 'validate', 'stringdist'

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'ada', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fastDummies', 'plyr', 'treeClust', 'data.table', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'corpcor', 'mclust'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doParallel', 'foreach'

Packages suggested but not available for checking: 'akima', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'skmeans', 'extraDistr', 'dplyr', 'Rfast', 'entropy', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
binary.state: no visible global function definition for 'runif'
dbn.dnn.train: no visible global function definition for 'runif'
dropout.mask: no visible global function definition for 'runif'
nn.train: no visible global function definition for 'runif'
rbm.train: no visible global function definition for 'runif'
sae.dnn.train: no visible global function definition for 'runif'
show.digit: no visible global function definition for 'gray'
show.digit: no visible global function definition for 'image'
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Biostrings', 'dplyr', 'ggplot2', 'ggthemes', 'keras', 'magrittr',
  'purrr', 'reticulate', 'rlang', 'seqinr', 'tensorflow'

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'knitr', 'rmarkdown', 'stringr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dirmult'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'evd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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:
  'Hmisc', 'SASxport', 'encode', 'spec', 'latexpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'lubridate', 'httr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'deSolve', 'gdata', 'gptk'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rJava'

Packages suggested but not available for checking:
  'DiagrammeR', 'roxygen2', 'protViz', 'shiny', 'testthat', 'knitr',
  'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/UserGuide.Rnw'
   'inst/doc/analysingExistingDatasets.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/UserGuide.Rnw'
   'vignettes/analysingExistingDatasets.Rnw'
(Is a VignetteBuilder field missing?)
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', 'covr'
Packages unavailable to check Rd xrefs: 'e1071', 'nloptr'
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: 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'igraph', 'future', 'rstackdeque', 'rlang', 'data.table',
  'assertthat', 'visNetwork', 'uuid', 'BBmisc', 'progress'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'shiny'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'polyclip'
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'dplyr', 'reshape2', 'stringr',
  'ggplot2', 'broom', 'coda', 'functional', 'kernlab', 'fastICA',
  'seriation', 'memoise', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'knitr', 'knitcitations', 'rmarkdown', 'formatR', 'extrafont',
  'testthat', 'svglite', 'VGAM'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Bchron'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'denpro'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'knitr'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fts', 'sfsmisc', 'vegan', 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rdpack'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'magrittr'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'officer', 'magrittr'

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', 'ftsa', 'rainbow', 'cobs', 'strucchange', 'RCurl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'shiny'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'leaps'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'fields', 'spam', 'ClusterR', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'ggplot2', 'viridis'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'seriation', 'colorspace', 'ape',
  'microbenchmark', 'gplots', 'heatmaply', 'dynamicTreeCut', 'pvclust',
  'corrplot', 'DendSer', 'fpc', 'circlize', 'covr'

Packages which this enhances but not available for checking:
  'ggdendro', 'dendroextras', 'Hmisc', 'data.table'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pspline', 'zoo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
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: 'forecast', 'pspline', 'zoo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'brnn', 'reshape2', 'scales', 'oce', 'MLmetrics', 'dplyr',
  'gridExtra', 'knitr', 'magrittr', 'plotly', 'randomForest', 'Cubist',
  'lubridate', 'psych', 'viridis'

Packages suggested but not available for checking:
  'testthat', 'dplR', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gclus', 'seriation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'RColorBrewer', 'gplots', 'seriation', 'gapmap', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'ggplot2', 'drc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Packages required but not available: 'irlba', 'FactoMineR'

Package suggested but not available for checking: 'missMDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'reshape2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'BH', 'RcppArmadillo', 'RcppEigen', 'RcppParallel',
  'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'changepoint'

Packages suggested but not available for checking:
  'pbapply', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'FNN', 'Rtsne', 'ggplot2', 'ggrepel', 'gridExtra',
  'RColorBrewer'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'histogram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'clime', 'gplots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'mvtnorm', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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
Skipping vignette re-building
Packages suggested but not available for checking:
  'data.table', 'testthat', 'usethis', 'devtools', 'roxygen2',
  'jsonlite', 'ggplot2', 'cowplot', 'directlabels', 'rmarkdown',
  'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'data.table'
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
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:
  'foreach', 'iterators', 'colorspace'
Errors in running code in vignettes:
when running code in 'DEoptim.Rnw'
  ...
> options(prompt = "R> ")

> rastrigin <- function(x) 10 * length(x) + sum(x^2 - 
+     10 * cos(2 * pi * x))

> library("colorspace")

  When sourcing 'DEoptim.R':
Error: there is no package called 'colorspace'
Execution halted

  'DEoptim.Rnw'... failed
  'DEoptimPortfolioOptimization.Rnw'... OK
Error(s) in re-building vignettes:
  ...
--- re-building 'DEoptim.Rnw' using Sweave

Error: processing vignette 'DEoptim.Rnw' failed with diagnostics:
 chunk 3 (label = figure1-code) 
Error in library("colorspace") : there is no package called 'colorspace'

--- failed re-building 'DEoptim.Rnw'

--- re-building 'DEoptimPortfolioOptimization.Rnw' using Sweave
--- finished re-building 'DEoptimPortfolioOptimization.Rnw'

SUMMARY: processing the following file failed:
  'DEoptim.Rnw'

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: 'robustbase'
Package unavailable to check Rd xrefs: 'DEoptim'
Packages required but not available: 'Rcpp', 'copula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'desc', 'dplyr', 'fs', 'ggplot2', 'Hmisc', 'magrittr', 'progress',
  'purrr', 'rlang', 'rms', 'rprojroot', 'stringr', 'telegram.bot',
  'tibble', 'tidyr', 'usethis'

Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'Rcpp', 'scales', 'plotly', 'magrittr', 'rmarkdown', 'htmlwidgets'

Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Rdonlp2'
Package required but not available: 'Rsolnp'

Packages suggested but not available for checking:
  'gamlss', 'gamlss.dist', 'Rdonlp2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'Rcpp', 'rrcov', 'np', 'sm', 'geometry', 'colorspace',
  'zoo', 'RcppArmadillo'

Packages suggested but not available for checking:
  'mvtnorm', 'rgl', 'sn', 'robustbase', 'dplyr', 'RcppArmadillo',
  'xts', 'covr', 'testthat', 'fda', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'abind', 'circular', 'rgl'

Package suggested but not available for checking: 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mnormt'

Packages suggested but not available for checking:
  'highlight', 'markdown', 'knitr', 'rmarkdown', 'ggplot2', 'dplyr',
  'tidyr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'ggplot2', 'dplyr', 'tidyr'

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:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'R6', 'crayon', 'rprojroot'

Packages suggested but not available for checking:
  'covr', 'testthat', 'whoami', 'withr', 'spelling', 'gh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'tibble', 'tidyr', 'purrr', 'broom', 'stringr',
  'haven', 'ggplot2', 'lmtest', 'rlang'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'ggplot2', 'plyr', 'scales', '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'
'LazyData' is specified without a 'data' directory
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', 'jsonlite', 'magrittr', 'RCurl', 'reshape'

Packages suggested but not available for checking:
  'curl', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'magrittr', 'rlang', 'scales', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'gridExtra', 'knitr', 'rmarkdown', 'testthat', 'vdiffr',
  'xplorerr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'exact2x2', 'DescTools', 'dplyr', 'rlang', 'tibble', 'stringr',
  'forcats', 'magrittr', 'tidyselect', 'scales', 'cli', 'kableExtra',
  'flextable', 'officer'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'tidyverse', 'here',
  'shiny', 'Exact'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'purrr', 'dplyr', 'tidyr', 'tibble', 'tidyselect',
  'forcats', 'cli', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'zoo', 'moments'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pander', 'dplyr', 'DT', 'htmltools'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'purrr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DescTools', 'rstudioapi', 'manipulate', 'writexl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'expm', 'Rcpp', 'rstudioapi', 'Exact', 'gld',
  'data.table', 'BH'

Packages suggested but not available for checking:
  'RDCOMClient', 'VGAM', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FitAR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reticulate', 'mnormt', 'fields', 'magrittr', 'plotly'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
arrayUpdate : pairUpdate: no visible global function definition for
  'runif'
conditionUpdate: no visible global function definition for 'runif'
designGG: no visible global function definition for 'runif'
experimentDesignTable: no visible global function definition for
  'write.csv'
plotAllScores: no visible global function definition for 'png'
plotAllScores: no visible global function definition for 'par'
plotAllScores: no visible global function definition for 'text'
plotAllScores: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off par png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Packages required but not available:
  'DeclareDesign', 'randomizr', 'fabricatr', 'estimatr', 'generics',
  'rlang', 'glue'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'slam', 'Rglpk'

Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'crossdes', 'dplyr', 'lme4'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'jsonlite', 'writexl', 'lmerTest', 'afex',
  'ggplot2', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'loglognorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'clue', 'combinat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'scatterplot3d', 'FME'
Package unavailable to check Rd xrefs: 'FME'
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking:
  'agridat', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clipr', 'desc', 'httr', 'knitr', 'magrittr', 'png', 'withr', 'xml2'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'sessioninfo', 'testthat', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stringr'

Packages suggested but not available for checking: 'testthat', 'generator'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'pbapply'

Packages suggested but not available for checking: 'dclone', 'dcmle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'signal', 'lavaan', 'doParallel', 'glasso', 'LogConcDEAD', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'iterators', 'itertools', 'ggplot2', 'reshape2', 'Rcpp',
  'gridExtra', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ROI', 'ROI.plugin.lpsolve', 'lpSolveAPI', 'pkgload'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'brglm2', 'AER',
  'ROI.plugin.ecos', 'ROI.plugin.glpk', 'ROI.plugin.neos',
  'ROI.plugin.alabama'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'robustbase', 'pcaPP', 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pROC', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'arrayhelpers', 'autothresholdr', 'checkmate', 'doParallel', 'dplyr',
  'filesstrings', 'foreach', 'ijtiff', 'iterators', 'magrittr', 'plyr',
  'purrr', 'Rcpp', 'RcppParallel', 'rlang', 'stringr', 'withr'

Packages suggested but not available for checking:
  'abind', 'covr', 'ggplot2', 'glue', 'gridExtra', 'knitr',
  'matrixStats', 'pacman', 'R.utils', 'rmarkdown', 'spelling',
  'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'robustbase', 'pcaPP', 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ash'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pheatmap', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'shiny', 'DT'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'minpack.lm'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'devRate-Ex.R' failed
The error most likely occurred in:

> ### Name: devRateQlBio
> ### Title: Biological likelihood of nls fits
> ### Aliases: devRateQlBio
> 
> ### ** Examples
> 
> myDf <- data.frame(temp = seq(from = 0, to = 50, by = 10),
+  rT = c(0.001, 0.008, 0.02, 0.03, 0.018, 0.004))
> myNLS <- list(
+  devRateModel(
+    eq = janisch_32,
+    df = myDf,
+    startValues = list(aa = 0.2, bb = 0.1, Dmin = 10, Topt = 30),
+    algo = "LM"),
+  devRateModel(
+    eq = kontodimas_04,
+    df = myDf,
+    startValues = list(aa = 1, Tmin = 7, Tmax = 40),
+    algo = "LM"),
+  devRateModel(
+    eq = poly2,
+    df = myDf,
+    startValues = list(a0 = 1, a1 = 1, a2 = 1),
+    algo = "LM"))
Error in loadNamespace(x) : there is no package called 'minpack.lm'
Calls: devRateModel ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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:
  'usethis', 'callr', 'cli', 'desc', 'ellipsis', 'fs', 'httr',
  'jsonlite', 'lifecycle', 'memoise', 'pkgbuild', 'pkgload',
  'rcmdcheck', 'remotes', 'rlang', 'roxygen2', 'rstudioapi',
  'rversions', 'sessioninfo', 'testthat', 'withr'

Packages suggested but not available for checking:
  'BiocManager', 'covr', 'curl', 'digest', 'DT', 'foghorn', 'gh',
  'gmailr', 'knitr', 'lintr', 'mockery', 'pingr', 'pkgdown', 'rhub',
  'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'DynTxRegime', 'modelObj'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dexter', 'shiny', 'shinyBS', 'DT', 'htmltools', 'htmlwidgets',
  'shinyjs', 'shinyFiles', 'jsonlite', 'dplyr', 'tidyr', 'tibble',
  'rlang', 'RCurl', 'DBI', 'readxl', 'writexl', 'readODS', 'ggplot2',
  'ggExtra', 'ggridges', 'networkD3', 'Cairo'

Packages suggested but not available for checking:
  'knitr', 'psych', 'sirt', 'MLCIRTwithin'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dexter', 'dplyr', 'RSQLite', 'rlang', 'igraph', 'tidyr',
  'DBI', 'crayon', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'mirt', 'ggplot2', 'Cairo'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RSQLite', 'DBI', 'tidyr', 'rlang', 'dplyr', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'latticeExtra', 'testthat', 'ggplot2', 'Cairo'

VignetteBuilder package required for checking but not installed: 'knitr'

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'sandwich', 'knitr', 'rmarkdown', 'spelling', 'formatR'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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: 'BH', 'Rcpp', 'RcppProgress'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'doParallel', 'foreach', 'ggplot2', 'fields', 'gplots', 'stringr',
  'data.table', 'gtools', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'iterators', 'testthat', 'itertools', 'latex2exp'

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.
Packages required but not available: 'dplyr', 'Formula'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'AER', 'mlogit', 'plm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'simex', 'mvtnorm', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'plyr', 'data.table', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RcppArmadillo', 'BH', 'RcppProgress', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplR', 'dplyr', 'forcats', 'ggplot2', 'ggpubr', 'magrittr', 'plyr',
  'purrr', 'rlang', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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: 'formula.tools'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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: 'Rcpp', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'ggplot2', 'dfcrm', 'PK', 'StanHeaders', 'BH',
  'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tmvtnorm', 'fda', 'ggplot2', 'plotly'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'chron'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Biobase', 'MLInterfaces', 'genefilter', 'ALL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'WGCNA', 'matrixStats'

Packages suggested but not available for checking:
  'knitr', 'impute', 'gplots', 'fdrtool', 'testthat', 'ggplot2',
  'plotrix', 'GOstats', 'HGNChelper', 'org.Hs.eg.db', 'AnnotationDbi',
  'abind', 'MEGENA', 'doMC', 'igraph', 'cowplot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'magrittr', 'stringr', 'GenomicRanges'

Packages suggested but not available for checking:
  'conflicted', 'dplyr', 'glue', 'knitr', 'rmarkdown', 'testthat',
  'biomaRt', 'edgeR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nloptr', 'COMPoissonReg', 'progress'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cvm.test : cvm.pval.disc: no visible global function definition for
  'integrate'
cvm.test : cvm.pval.disc: no visible global function definition for
  'dchisq'
cvm.test : cvm.pval.disc: no visible global function definition for
  'nlm'
cvm.test : cvm.stat.disc: no visible global function definition for
  'knots'
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  'knots'
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  'runif'
cvm.test: no visible global function definition for 'is.stepfun'
cvm.test: no visible global function definition for 'knots'
ks.test : exact.pval : ts.pval: no visible global function definition
  for 'ecdf'
ks.test : sim.pval: no visible global function definition for 'runif'
ks.test : sim.pval : getks: no visible global function definition for
  'ecdf'
ks.test: no visible global function definition for 'is.stepfun'
ks.test: no visible global function definition for 'knots'
ks.test: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rgl'

Packages suggested but not available for checking:
  'RColorBrewer', 'knitr', 'rmarkdown', 'data.table', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'gap', 'lmtest', 'ape', 'qgam', 'lme4'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'sfsmisc', 'glmmTMB', 'spaMM',
  'GLMMadaptive'

VignetteBuilder package required for checking but not installed: 'knitr'

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: 'VennDiagram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'forecast', 'future.apply', 'future', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape', 'survey', 'haven', 'matrixStats', 'dplyr', 'rlang',
  'crayon'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'gridExtra', 'coda', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'meta', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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', 'downloader', 'glue', 'htmltools', 'htmlwidgets', 'igraph',
  'influenceR', 'magrittr', 'purrr', 'RColorBrewer', 'readr', 'rlang',
  'rstudioapi', 'scales', 'stringr', 'tibble', 'tidyr', 'viridis',
  'visNetwork'

Packages suggested but not available for checking:
  'covr', 'DiagrammeRsvg', 'rsvg', 'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rJava'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dialrjars', 'rJava'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'knitr', 'pillar', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'scales', 'glue', 'purrr', 'tibble', 'rlang', 'withr', 'DiceDesign',
  'dplyr', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'covr', 'kernlab', 'xml2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringdist', 'vegan', 'ggplot2', 'tidyr', 'data.table', 'purrr',
  'stringr', 'tibble'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rgl', 'randtoolbox'
Package required but not available: 'DiceKriging'

Packages suggested but not available for checking:
  'gam', 'akima', 'mda', 'polspline'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rgenoud', 'foreach', 'doParallel', 'testthat', 'numDeriv'
Package unavailable to check Rd xrefs: 'rgenoud'
Running examples in 'DiceKriging-Ex.R' failed
The error most likely occurred in:

> ### Name: cv
> ### Title: Multiple fold cross validation for a km object
> ### Aliases: cv
> ### Keywords: models
> 
> ### ** Examples
> 
> # -------------------------------------------------
> # A 1D example illustrating leave-one-out residuals 
> # and their correlation 
> # -------------------------------------------------
> 
> # Test function (From Xiong et al. 2007; See scalingFun's doc) 
> myfun <- function(x){ 
+   sin(30 * (x - 0.9)^4) * cos(2 * (x - 0.9)) + (x - 0.9) / 2
+ }
> t <- seq(from = 0, to = 1, by = 0.005)
> allresp <- myfun(t)
> par(mfrow = c(1, 1), mar = c(4, 4, 2, 2))
> plot(t, allresp, type = "l")
> 
> # Design points and associated responses 
> nn <- 10
> design <- seq(0, 1, length.out = nn)
> y <- myfun(design)
> points(design, y, pch = 19)
> 
> # Model definition and GP prediction (Kriging)
> set.seed(1)
> model1 <- km(design = data.frame(design = design), 
+              response = data.frame(y = y), nugget = 1e-5,
+              multistart = 10, control = list(trace = FALSE))
Error in f(model, envir = envir.logLik) : Package "foreach" not found
Calls: km -> f
Execution halted
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:
  'DiceKriging', 'randtoolbox', 'pbivnorm', 'rgenoud', 'mnormt',
  'DiceDesign'

Packages suggested but not available for checking: 'KrigInv', 'GPareto'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'assertthat', 'clue', 'clusterCrit', 'clValid', 'dplyr',
  'ggplot2', 'infotheo', 'klaR', 'magrittr', 'mclust', 'NMF', 'purrr',
  'RankAggreg', 'Rcpp', 'stringr', 'tidyr', 'yardstick'

Packages suggested but not available for checking:
  'apcluster', 'covr', 'dbscan', 'e1071', 'kernlab', 'knitr',
  'kohonen', 'pander', 'poLCA', 'progress', 'RColorBrewer',
  'rmarkdown', 'Rtsne', 'sigclust', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DiceKriging', 'DiceEval', 'DiceDesign', 'R.cache', 'geometry',
  'scatterplot3d'

Package which this enhances but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dichromat: no visible global function definition for 'col2rgb'
dichromat: no visible global function definition for 'predict'
dichromat: no visible global function definition for 'rgb'
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for 'txtProgressBar'
le.pesquisa: no visible global function definition for 'type.convert'
le.pesquisa: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
Note: found 2297 marked UTF-8 strings
Package required but not available: 'matlabr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpSolveAPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'dplyr', 'magrittr', 'purrr', 'rlang'

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'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'foreach', 'igraph', 'stringi', 'RCurl', 'splitstackshape',
  'data.table', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fixest', 'plotrix', 'stringr', 'sampling', 'assertthat'

Package suggested but not available for checking: 'wooldridge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BMisc', 'pbapply', 'ggplot2', 'ggpubr', 'DRDID', 'knitr'

Packages suggested but not available for checking:
  'rmarkdown', 'plm', 'here'

VignetteBuilder package required for checking but not installed: 'knitr'

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.
Packages required but not available: 'flux', 'fmsb', 'ggplot2', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggplot2'
Malformed Title field: should not end in a period.
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.
L2eV: no visible binding for global variable 'constants'
L2w: no visible binding for global variable 'constants'
dielectric: no visible global function definition for 'new'
dielectric2plot: no visible global function definition for 'reshape'
eV2L: no visible binding for global variable 'constants'
t2eV: no visible binding for global variable 'constants'
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'brew', 'httr', 'jsonlite'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mboost', 'penalized', 'stabs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gplots', 'stringr', 'data.table', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'pcaMethods', 'igraph', 'fdrtool', 'multtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gee', 'rootSolve', 'PropCIs'

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', 'lubridate', 'knitr', 'rmarkdown', 'purrr', 'dplyr',
  'stringi', 'stringr', 'devtools', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'pcaPP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'here', 'rlang', 'stringr', 'reshape2',
  'ggnewscale'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'diagram'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'JuliaCall', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgdal', 'raster', 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'igraph', 'progress', 'Rcpp', 'sf', 'dplyr',
  'data.table'

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', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'qlcMatrix', 'data.table', 'Hmisc', 'gplots', 'igraph',
  'lsa', 'foreach', 'doParallel', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crayon'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gsl'

Packages suggested but not available for checking:
  'randomNames', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/bernstein.Rnw'
   'inst/doc/diffpriv.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'htmlwidgets'

Package suggested but not available for checking: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'scatterplot3d', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dfoptim', 'nloptr', 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'rgl', 'colorspace'

Packages suggested but not available for checking:
  'knitr', 'coda', 'fptdApprox', 'Quandl', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'rgl', 'colorspace'

Packages suggested but not available for checking:
  'DiffusionRgqd', 'DiffusionRjgqd', 'knitr', 'coda', 'Quandl', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'rgl', 'colorspace'

Packages suggested but not available for checking:
  'DiffusionRgqd', 'knitr', 'coda', 'Quandl', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'igraph', 'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'lintr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'jsonlite'

Packages suggested but not available for checking: 'covr', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pander', 'Rdpack'

Packages suggested but not available for checking:
  'Ckmeans.1d.dp', 'FunChisq', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'grplasso', 'penalized', 'miscTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'calculus', 'CTT', 'ggplot2', 'msm', 'plyr', 'reshape2', 'VGAM'

Package suggested but not available for checking: 'ShinyItemAnalysis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'TestDataImputation', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mirt', 'ltm', 'lme4', 'deltaPlotR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'difR', '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:
  'penalized', 'VGAM', 'gridBase', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'tinytest', 'knitr', 'rmarkdown', 'minidown'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'readbitmap'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'bibliometrix', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rlang'

Packages suggested but not available for checking:
  'folio', 'FactoMineR', 'ggrepel', 'khroma', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'hnp', 'rootSolve'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'minpack.lm', 'numDeriv', 'forecast', 'reshape2', 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DRR', 'magrittr'

Packages suggested but not available for checking:
  'NMF', 'RANN', 'RSpectra', 'Rtsne', 'cccd', 'coRanking',
  'diffusionMap', 'energy', 'fastICA', 'ggplot2', 'igraph', 'keras',
  'kernlab', 'knitr', 'lle', 'loe', 'optimx', 'pcaL1', 'pcaPP',
  'reticulate', 'rgl', 'scales', 'scatterplot3d', 'tensorflow',
  'testthat', 'tidyr', 'tinytex', 'umap', 'vegan'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/dimensionality-reduction.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'simcdm', 'Rcpp', 'RcppArmadillo', 'rgen'

Packages suggested but not available for checking:
  'CDM', 'covr', '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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'lubridate', 'rmarkdown', 'scales',
  'testthat', 'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'
scale_date_ym: no visible binding for global variable 'date_ym_trans'
scale_date_yq: no visible binding for global variable 'date_yq_trans'
scale_date_yw: no visible binding for global variable 'date_yw_trans'
Undefined global functions or variables:
  date_ym_trans date_yq_trans date_yw_trans
Packages unavailable to check Rd xrefs: 'lubridate', 'zoo', 'scales', 'ggplot2'
'LazyData' is specified without a 'data' directory
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: 'limma', 'WGCNA', 'ggplot2'

Package suggested but not available for checking: 'edgeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'partykit', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'usethis', 'ggplot2', 'lemon', 'gridExtra', 'dplyr', 'DWDLargeR',
  'SparseM', 'sampling'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'R6', 'shiny', 'cli', 'stringr', 'jsonlite',
  'future', 'future.apply', 'progressr', 'fastmap', 'base64url',
  'base64enc', 'synchronicity', 'digest', 'rlang', 'startup',
  'rstudioapi'

Packages suggested but not available for checking:
  'microbenchmark', 'htmltools', 'knitr', 'rmarkdown', 'testthat',
  'promises', 'magrittr', 'glue', 'yaml', 'qs', 'RcppRedis',
  'future.callr', 'remotes'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'liqueueR', 'plyr', 'mvnfast'

Package suggested but not available for checking: 'optmatch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
aLine: no visible global function definition for 'lines'
aLine: no visible global function definition for 'ecdf'
dip.test: no visible global function definition for 'complete.cases'
dip.test: no visible global function definition for 'runif'
dip.test: no visible global function definition for 'approx'
plot.dip: no visible global function definition for 'par'
plot.dip: no visible global function definition for 'ecdf'
plot.dip: no visible global function definition for 'title'
plot.dip: no visible global function definition for 'abline'
plot.dip: no visible global function definition for 'axis'
plot.dip: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par runif title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
Packages required but not available: 'glmnet', 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'scales'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sandwich', 'Formula', 'glue'

Packages suggested but not available for checking:
  'knitr', 'dplyr', 'ggplot2', 'reshape2', 'scales', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigstatsr', 'doParallel', 'foreach', 'RANN', 'Rfast', 'Rfast2',
  'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quadprog'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'inlinedocs', 'RColorBrewer', 'ggplot2',
  'rlang', 'alphahull', 'lars', 'latticeExtra', 'dplyr', 'ggthemes',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'collapsibleTree', 'data.tree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'calibrate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'minqa', 'foreach', 'iterators', 'haven', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'withr', 'doParallel', 'EdSurvey'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'ggplot2', 'mvtnorm'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'maxLik'

Packages suggested but not available for checking:
  'rgl', 'knitr', 'formatR', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mcmcse'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
nullTest: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
simPop: no visible global function definition for 'rnorm'
simPop: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
Packages required but not available: 'movMF', 'rotasym'

Package suggested but not available for checking: 'viridisLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maptools', 'raster', 'foreach', 'sp', 'doParallel', 'rgeos',
  'splancs', 'rgdal', 'TMB', 'dplyr', 'ggplot2', 'cowplot',
  'sparseMVN', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'INLA', 'knitr', 'rmarkdown', 'SpatialEpi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rmarkdown', 'scales', 'shiny'

Packages suggested but not available for checking:
  'shinytest', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SingleCellExperiment', 'TSCAN', 'httr', 'mclust', 'statmod',
  'igraph', 'RWeka', 'philentropy', 'NetIndices', 'png', 'readr',
  'RColorBrewer', 'ggplot2', 'fpc', 'rpart.plot', 'tsne',
  'AnnotationDbi', 'org.Hs.eg.db', 'impute'

Packages suggested but not available for checking: 'testthat', 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crul', 'jsonlite', 'xml2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lmom', 'ggplot2', 'CircStats', 'checkmate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'disclap', 'RcppProgress'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'gridExtra', 'ggdendro', 'scales', 'seriation',
  'fwsim', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
rdisclap: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available:
  'lavaan', 'arules', 'sirt', 'pbivnorm', 'psych'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tmod', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'magrittr', 'rlang', 'janitor', 'broom'

Packages suggested but not available for checking:
  'NlsyLinks', 'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'ggpubr', 'GGally', 'network', 'ggplot2', 'dplyr',
  'ggrepel', 'BiocManager', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'ngram', 'readr', 'stringdist', 'stringi',
  'stopwords', 'synthesisr', 'tm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'rlang', 'golem', 'shiny', 'scales', 'config', 'plotly',
  'ggplot2', 'shinyjs', 'shinyAce', 'ggdendro', 'echarts4r',
  'htmltools', 'htmlwidgets', 'colourpicker', 'shinydashboard',
  'shinycustomloader', 'shinydashboardPlus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'sparsebnUtils', 'igraph', 'RcppEigen'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'R.rsp', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'R.rsp', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rsolnp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
p.discrete.adjust : <anonymous>: no visible global function definition
  for 'stepfun'
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
Packages suggested but not available for checking: 'coin', 'exactRankTests'
'LazyData' is specified without a 'data' directory
Package required but not available: 'plyr'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rsolnp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
value: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Package suggested but not available for checking: 'FactoMineR'
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'parsnip', 'purrr', 'rlang', 'tibble', 'withr', 'dials'

Packages suggested but not available for checking:
  'testthat', 'mda', 'klaR', 'earth', 'mlbench', 'covr', 'ggplot2',
  'xml2', 'spelling', 'naivebayes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'functional', 'mvtnorm', 'data.table'

Packages suggested but not available for checking:
  'matrixcalc', 'numDeriv', 'caret', 'Ecdat', 'pec', 'randomForest',
  'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'sf', 'terra', 'raster', 'rgdal', 'mapview'

VignetteBuilder package required for checking but not installed: 'knitr'
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 required but not available: 'sp'

Packages suggested but not available for checking:
  'spdep', 'geostatsp', 'mapmisc', 'knitr'

Packages which this enhances but not available for checking: 'INLA', 'XML'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/bym.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bbmle', 'dplyr', 'magrittr', 'rlang', 'systemfit', 'tibble',
  'tidyr', 'png', 'Rcpp', 'RcppGSL', 'RcppParallel'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'numDeriv', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'optimr', 'Formula', 'numDeriv'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'sandwich'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'matrixStats'

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.
Packages required but not available:
  'dplyr', 'rlang', 'tidyselect', 'purrr', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'forcats', 'scales'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'Rcpp', 'glue', 'rlang', 'future.apply', 'fs',
  'jsonlite', 'pryr', 'stringr', 'fst', 'globals', 'future',
  'data.table', 'crayon', 'bigreadr', 'furrr', 'bit64', 'benchmarkme'

Packages suggested but not available for checking:
  'testthat', 'nycflights13', 'magrittr', 'shiny', 'LaF', 'readr',
  'rstudioapi', 'biglm', 'biglmm', 'speedglm', 'broom', 'ggplot2',
  'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'zoo', 'subplex'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'sp', 'Rcpp'

Packages suggested but not available for checking:
  'rJava', 'terra', 'rgdal', 'rgeos', 'XML', 'ROCR', 'deldir', 'gstat',
  'randomForest', 'kernlab', 'maptools', 'jsonlite', 'gbm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

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: 'car'
Package unavailable to check Rd xrefs: 'car'
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ape', 'ade4', 'castor', 'Claddis', 'geiger', 'geometry', 'geoscale',
  'mnormt', 'phangorn', 'phyclust', 'vegan', 'scales'

Packages suggested but not available for checking: 'testthat', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'sp', 'raster', 'plyr', 'dplyr', 'foreach', 'magrittr',
  'viridis'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'randomForest', 'Cubist', 'gam'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sfsmisc', 'matrixcalc', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
densest: no visible global function definition for 'weighted.mean'
diss: no visible global function definition for 'cov'
neighbors: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
Packages required but not available: 'mrds', 'dplyr', 'rlang'

Packages suggested but not available for checking:
  'covr', 'progress', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: '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:
  'plyr', 'foreach', 'doParallel', 'fields', 'viridis', 'RColorBrewer',
  'data.table', 'iterators', 'arrangements'

Packages suggested but not available for checking:
  'devtools', 'formatR', 'kableExtra', 'magrittr', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'prettyGraphs', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'httr', 'digest', 'jsonlite', 'stringr', 'R6'

Packages suggested but not available for checking:
  'opencpu', 'knitr', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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: 'sn', 'emmeans'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rmarkdown', 'bookdown', 'xfun', 'htmltools', 'jsonlite',
  'lubridate', 'png', 'mime', 'rstudioapi', 'rprojroot', 'xml2',
  'base64enc', 'whisker', 'stringr', 'knitr', 'digest', 'yaml',
  'openssl', 'downlit'

Packages suggested but not available for checking:
  'htmlwidgets', 'progress', 'r2d3', 'DiagrammeR', 'shiny',
  'rsconnect', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'proxy', 'dplyr', 'assertthat', 'fastmatch', 'tidyr', 'factoextra',
  'ggplot2', 'broom', 'fastcluster', 'pbapply'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'R6', 'R62S3', 'set6', 'Rcpp'

Packages suggested but not available for checking:
  'cubature', 'GoFKernel', 'knitr', 'testthat', 'rmarkdown',
  'magrittr', 'extraDistr', 'actuar', 'plotly', 'pracma'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'distr', 'distrEx', 'distrSim', 'distrTEst', 'distrTeach', 'RandVar',
  'distrMod', 'startupmsg'

Packages suggested but not available for checking: 'Biobase', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/distr.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'bamlss', 'gamlss', 'gamlss.dist', 'ggplot2',
  'rhandsontable', 'magrittr', 'formatR', 'betareg'

Packages suggested but not available for checking:
  'testthat', 'gridExtra', 'glogis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'setRNG', 'distr', 'distrEx', 'distrSim', 'startupmsg'

Packages suggested but not available for checking: 'distrMod', 'distrTEst'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'distr', 'startupmsg'

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', 'httr', 'jsonlite', 'plumberDeploy', 'analogsea'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vctrs', 'rlang', 'generics', 'ellipsis', 'numDeriv', 'ggplot2',
  'scales', 'farver', 'digest', 'lifecycle'

Packages suggested but not available for checking:
  'testthat', 'covr', 'mvtnorm', 'actuar', 'ggdist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', 'doParallel', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'GA', 'AdaptGauss', 'pracma'

Package suggested but not available for checking: 'parallelDist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ellipsis', 'glue'

Packages suggested but not available for checking:
  'covr', 'cowplot', 'ggplot2', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rdpack', 'flexmix', 'modeltools'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GeneralizedHyperbolic', 'VarianceGamma', 'SkewHyperbolic', 'RUnit'
Packages unavailable to check Rd xrefs: 'GeneralizedHyperbolic', 'VarianceGamma'
Running examples in 'DistributionUtils-Ex.R' failed
The error most likely occurred in:

> ### Name: momIntegrated
> ### Title: Moments Using Integration
> ### Aliases: momIntegrated
> ### Keywords: distribution univar
> 
> ### ** Examples
> 
> require(GeneralizedHyperbolic)
Loading required package: GeneralizedHyperbolic
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'GeneralizedHyperbolic'
> ### Calculate the mean of a generalized hyperbolic distribution
> ### Compare the use of integration and the formula for the mean
> m1 <- momIntegrated("ghyp", param = c(0, 1, 3, 1, 1 / 2), order = 1, about = 0)
Error in momIntegrated("ghyp", param = c(0, 1, 3, 1, 1/2), order = 1,  : 
  Relevant package must be loaded
Execution halted
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Package which this enhances but not available for checking: 'RobExtremes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
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: 'startupmsg', 'sfsmisc'

Packages suggested but not available for checking:
  'distrEx', 'svUnit', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
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(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'distr', 'fBasics', 'fGarch', 'startupmsg'

Packages suggested but not available for checking: 'distrEx', 'distrMod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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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:
  'DBI', 'digest', 'glue', 'testthat', 'lifecycle'

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  'withr', 'rmarkdown', 'lintr'

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'ggpubr', 'scales', 'sgeostat', 'rms', 'MapGAM',
  'gam', 'rlang', 'RColorBrewer', 'RcppEigen'

Packages suggested but not available for checking: 'testthat', 'BOLTSSIRR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'jsonlite', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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manual.
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  'RJDBC', 'RJSONIO', 'RPostgres', 'shiny', 'shinyjs', 'xml2'

Packages suggested but not available for checking: 'lintr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'httr', 'jsonlite', 'purrr', 'stringr',
  'tibble'

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  'strucchange', 'wavethresh', 'roll', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'corrplot', 'dplyr', 'extrafont', 'ggplot2', 'gridExtra',
  'hrbrthemes', 'kableExtra', 'knitr', 'magrittr', 'mice', 'partykit',
  'prettydoc', 'purrr', 'RcmdrMisc', 'rlang', 'rmarkdown', 'tibble',
  'tidyr', 'tidyselect'

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manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'dplyr', 'magrittr', 'ggplot2', 'stringr', '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: '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:
  'abind', 'bayesplot', 'coda', 'ggplot2', 'ggrepel', 'MCMCpack',
  'modeltools', 'pcaPP', 'robustbase', 'Rcpp', 'RcppArmadillo',
  'RcppProgress'

Packages suggested but not available for checking:
  'knitr', 'mcmcplots', 'rlecuyer', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DEoptim', 'Rcpp', 'dplyr', 'optimr', 'pbapply', 'tidyr', 'BH'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'readxl', 'xml2', 'rlang', 'rmarkdown', 'knitr',
  'digest', 'writexl', 'rappdirs', 'yaml', 'EML', 'stringr'

Packages suggested but not available for checking:
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  'openxlsx'

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'sp', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nadiv', 'robustbase', 'pls'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cOde', 'deSolve', 'rootSolve', 'ggplot2', 'stringr', 'plyr',
  'dplyr', 'foreach', 'doParallel'

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'lifecycle', 'magrittr', 'memoise', 'pillar', 'purrr', 'rlang',
  'tibble', 'tidyr', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
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  'digest', 'fansi', 'keyring', 'knitr', 'mockr', 'nycflights13',
  'odbc', 'RMariaDB', 'rmarkdown', 'RPostgres', 'RSQLite', 'testthat',
  'tidyverse', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'grpreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'glmnet', 'kernlab', 'ks', 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'readxl', 'purrr', 'lubridate', 'httr', 'tidyr',
  'tibble', 'progress'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xts', 'zoo', 'quantmod', 'dplyr', 'readr', 'DBI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'igraph', 'lars'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rnw' using Sweave
dna 2.1-2 loaded

Attaching package: 'dna'

The following object is masked from 'package:base':

    summary

Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "Introduction.tex" --max-iterations=20 -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/tex/latex" -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'Introduction.Rnw' failed with diagnostics:
running 'texi2dvi' on 'Introduction.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex (file ./Introduction-003.pdf): PDF inclusion: required 
page does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!

--- failed re-building 'Introduction.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'spdep', 'fdrtool', 'GOstats', 'locfdr', 'mvtnorm',
  'caTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'gplots', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Files named as vignettes but with no recognized vignette engine:
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(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

Packages suggested but not available for checking:
  'gtools', 'MCMCpack', 'functional'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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manual.
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  'dplyr'

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VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
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   'inst/doc/linest-lsmeans.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tm', 'quanteda', 'ggplot2', 'glmnet', 'stringr', 'dplyr', 'english',
  'textstem', 'SnowballC', 'stringi'

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'officer', 'nortest', 'flextable', 'broom', 'tictoc', 'DescTools',
  'magrittr', 'dplyr', 'plotrix', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'officer', 'nortest', 'flextable', 'broom', 'tictoc', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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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
Packages suggested but not available for checking:
  'copula', 'numDeriv', 'Deriv', 'cubature', 'SparseGrid', 'mvtnorm',
  'testthat'
Packages unavailable to check Rd xrefs: 'Deriv', 'cubature', 'SparseGrid', 'numDeriv'
'LazyData' is specified without a 'data' directory
Running examples in 'docopulae-Ex.R' failed
The error most likely occurred in:

> ### Name: nint_integrateNCube
> ### Title: Integrate Hypercube
> ### Aliases: nint_integrateNCube nint_integrateNCube_integrate
> ###   nint_integrateNCube_cubature nint_integrateNCube_SparseGrid
> 
> ### ** Examples
> 
> ## integrate with defaults (stats::integrate)
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
[1] 1.414214
> 
> 
> dfltNCube = nint_integrateNCube
> 
> ## prepare for integrateA
> ncube = function(f, lowerLimit, upperLimit, ...) {
+     cat('using integrateA\n')
+     integrateA(f, lowerLimit, upperLimit, ..., subdivisions=2)
+ }
> ncube = nint_integrateNCube_integrate(ncube)
> unlockBinding('nint_integrateNCube', environment(nint_integrate))
> assign('nint_integrateNCube', ncube, envir=environment(nint_integrate))
> 
> ## integrate with integrateA
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
using integrateA
[1] 1.414214
> 
> 
> ## prepare for cubature
> ncube = function(f, lowerLimit, upperLimit, ...) {
+     cat('using cubature\n')
+     r = cubature::adaptIntegrate(f, lowerLimit, upperLimit, ..., maxEval=1e3)
+     return(r$integral)
+ }
> unlockBinding('nint_integrateNCube', environment(nint_integrate))
> assign('nint_integrateNCube', ncube, envir=environment(nint_integrate))
> 
> ## integrate with cubature
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
using cubature
Error in loadNamespace(x) : there is no package called 'cubature'
Calls: nint_integrate ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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: 'roxygen2'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ppert: no visible global function definition for 'pbeta'
prepare8pkg: no visible global function definition for 'glob2rx'
qpert: no visible global function definition for 'qbeta'
rpert: no visible global function definition for 'rbeta'
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
Packages required but not available:
  'officer', 'magrittr', 'htmltools', 'xml2', 'yaml'

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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'checkmate', 'desc', 'rcmdcheck', 'roxygen2', 'rstudioapi',
  'withr'

Packages suggested but not available for checking:
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  'rprojroot', 'RUnit', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'drat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'purrr', 'rlang', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'rprojroot', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking: 'covr', 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'digest', 'magrittr', 'osmdata', 'Rcpp', 'RcppParallel',
  'RcppThread'

Packages suggested but not available for checking:
  'dplyr', 'geodist', 'ggplot2', 'igraph', 'igraphdata', 'jsonlite',
  'knitr', 'purrr', 'rbenchmark', 'RColorBrewer', 'rmarkdown',
  'roxygen2', 'scales', 'sf', 'testthat', 'tidygraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'conf.design', 'vcd', 'combinat', 'numbers', 'partitions'

Packages suggested but not available for checking:
  'FrF2', 'DoE.wrapper', 'RColorBrewer'

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.
Packages required but not available: 'combinat', 'DoE.base'

Package suggested but not available for checking: 'slam'

Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DoE.wrapper'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FrF2', 'DoE.base', 'rsm', 'lhs', 'DiceDesign', 'AlgDesign'

Package suggested but not available for checking: 'skpr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'foreach', 'future', 'globals', 'iterators'

Packages suggested but not available for checking:
  'doRNG', 'markdown', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'lme4', 'testthat', 'car', 'covr', 'knitr', 'rmarkdown', 'pscl',
  'dynlm', 'ggplot2', 'reshape2', 'betareg', 'performance'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'igraph', 'chron'

Packages suggested but not available for checking:
  'XLConnect', 'openxlsx', 'RcmdrMisc'

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
Packages suggested but not available for checking:
  'dominanceanalysis', 'relaimpo', 'yhat'
Packages required but not available: 'foreach', 'iterators', 'Rmpi'

Packages suggested but not available for checking:
  'randomForest', 'itertools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'RANN', 'nabor'
'LazyData' is specified without a 'data' directory
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: 'foreach', 'iterators'

Packages suggested but not available for checking:
  'caret', 'mlbench', 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'dm', 'knitr', 'rmarkdown', 'conflicted', 'purrr', 'readr', 'readxl',
  'rvest', 'sqldf', 'stringr', 'tidyr', 'tibble', 'testthat',
  'usethis', 'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'plyr', 'tmcn', 'tidyselect', 'reshape2', 'tidyr',
  'rvest', 'xml2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'data.table', 'lme4', 'ggplot2', 'gridExtra', 'lmerTest',
  'deSolve', 'futile.logger'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'rngtools', 'iterators'

Packages suggested but not available for checking:
  'doParallel', 'doMPI', 'doRedis', 'rbenchmark', 'devtools', 'knitr',
  'bibtex', 'testthat', 'pkgmaker'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/doRNG.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sensitivity2x2xk', 'sensitivitymult', 'sensitivitymv', 'senstrat'

Packages suggested but not available for checking: 'optmatch', 'DiPs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'igraph', 'dagitty'

Package suggested but not available for checking: 'DOT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking:
  'numDeriv', 'Rsolnp', 'quadprog', 'multcomp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'iterators', 'snow'

Packages suggested but not available for checking:
  'RUnit', 'caret', 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'optmatch'
Package required but not available: 'mvmeta'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rms'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/dosresmeta.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'plyr', 'testthat'
dostats: no visible binding for global variable 'na.fail'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
pval.default: no visible global function definition for '.hasSlot'
pval.lm: no visible global function definition for 'anova'
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package unavailable to check Rd xrefs: 'plyr'
Running examples in 'dostats-Ex.R' failed
The error most likely occurred in:

> ### Name: dostats
> ### Title: Convenient interface for computing statistics on a vector
> ### Aliases: dostats
> ### Keywords: misc utilities,
> 
> ### ** Examples
> 
> data(mtcars)
> library(plyr)
Error in library(plyr) : there is no package called 'plyr'
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 suggested but not available for checking:
  'microbenchmark', 'OpenMPController', 'RColorBrewer', 'roxygen2',
  'spam', 'testthat'
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
Packages required but not available: 'ggplot2', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'htmltools'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'broomExtra', 'margins', 'dplyr', 'stringr', 'ggstance',
  'rlang', 'purrr', 'gtable'

Packages suggested but not available for checking:
  'ordinal', 'tibble', 'gridExtra', 'knitr', 'rmarkdown', 'broom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'coneproj'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'data.table', 'checkmate', 'mlr3', 'mlr3tuning', 'mvtnorm',
  'clusterGeneration', 'readstata13', 'mlr3learners'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'patrick', 'paradox',
  'dplyr', 'glmnet', 'lgr', 'ranger', 'sandwich', 'AER', 'bbotk'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'unglue'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bootstrap', 'forecast'

Packages suggested but not available for checking:
  'PerformanceAnalytics', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'brio', 'digest', 'evaluate', 'fansi', 'rlang', 'vctrs', 'yaml'

Packages suggested but not available for checking:
  'rmarkdown', 'jsonlite', 'testthat', 'covr', 'pkgload', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'digest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fs', 'readr', 'writexl', 'bsplus', 'mime', 'htmltools', 'base64enc',
  'magrittr', 'zip', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstack', 'dplyr', 'magrittr', 'keras', 'raster',
  'tensorflow', 'sp', 'rgdal', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'R.utils'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sem', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'digest'

Packages suggested but not available for checking:
  'rex', 'covr', 'testthat', 'knitr', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tmvtnorm', 'VGAM', 'gplots', 'CEoptim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dbscan', 'e1071', 'exactci', 'ggplot2', 'ggpubr', 'raster', 'rlist',
  'scales', 'shiny', 'shinyjs', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'VGAM', 'gsl', 'moments', 'fitdistrplus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'matrixStats', 'png', 'R.utils', 'stringi', 'stringr',
  'XML', 'plyr', 'signal'

Packages suggested but not available for checking:
  'Biobase', 'Cairo', 'dichromat', 'foreach', 'forecast', 'gmp',
  'iterators', 'knitr', 'RColorBrewer', 'testthat', 'tikzDevice',
  'waveslim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'miniUI', 'rstudioapi', 'shinyWidgets', 'shinyAce',
  'tidyverse', 'tidyr', 'stringr', 'magrittr', 'plyr', 'DT'

Packages suggested but not available for checking:
  'nycflights13', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ellipsis', 'generics', 'glue', 'lifecycle', 'magrittr', 'R6',
  'rlang', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'bench', 'broom', 'callr', 'covr', 'DBI', 'dbplyr', 'knitr',
  'Lahman', 'lobstr', 'microbenchmark', 'nycflights13', 'purrr',
  'rmarkdown', 'RMySQL', 'RPostgreSQL', 'RSQLite', 'testthat', 'tidyr',
  'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'dbplyr', 'odbc', 'bit64', 'DBI'

Packages suggested but not available for checking:
  'blob', 'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'httr', 'jsonlite', 'magrittr', '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: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'coda'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DPQ', 'Rmpfr', 'gmp'

Package suggested but not available for checking: 'sfsmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sfsmisc'

Packages suggested but not available for checking:
  'Rmpfr', 'scatterplot3d', 'akima'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'markdown', 'knitr', 'htmltools', 'RcppDynProg', 'microbenchmark',
  'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCMCpack', 'plyr', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'truncdist', 'binaryLogic', 'prodlim', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH', 'sitmo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'matrixcalc', 'tensor', 'Rdpack'

Packages suggested but not available for checking:
  'drc', 'devtools', 'roxygen2', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'testthat', 'spelling'

Package which this enhances but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'config', 'golem', 'shiny', 'DT', 'ggplot2', 'readr', 'openxlsx',
  'dplyr', 'RColorBrewer', 'stringr', 'tidyr', 'purrr', 'tibble',
  'broom', 'cowplot', 'ggforce', 'magrittr', 'shinydashboard',
  'shinyWidgets', 'colourpicker', 'colorspace', 'visNetwork', 'igraph',
  'rlang', 'htmltools', 'promises', 'future', 'lubridate', 'xml2',
  'rvest', 'curl', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'processx', 'knitr', 'zip', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'tidyr', 'tibble', 'dplyr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 78 marked UTF-8 strings
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: 'htmlwidgets', 'shiny', 'shinyjs'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64url', 'digest', 'igraph', 'rlang', 'storr', 'tidyselect',
  'txtq', 'vctrs'

Packages suggested but not available for checking:
  'abind', 'bindr', 'callr', 'cli', 'clustermq', 'crayon', 'curl',
  'data.table', 'disk.frame', 'downloader', 'fst', 'future', 'ggplot2',
  'ggraph', 'keras', 'knitr', 'lubridate', 'networkD3', 'prettycode',
  'progress', 'qs', 'Rcpp', 'rmarkdown', 'rstudioapi', 'styler',
  'testthat', 'tibble', 'txtplot', 'usethis', 'visNetwork', 'webshot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'readr', 'data.table', 'httr', 'git2r', 'xml2',
  'tokenizers', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'fmsb', 'knitr', 'magrittr', 'highcharter', 'rmarkdown',
  'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'git2r', 'knitr', 'rmarkdown', 'minidown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'git2r'
Running 'simpleTests.R'
  Running 'skeleton_git2r.R'
Running the tests in 'tests/skeleton_git2r.R' failed.
Last 13 lines of output:
  [4] "foo/Read-and-delete-me" "foo/man/foo-package.Rd"
  building
  * checking for file 'foo/DESCRIPTION' ... OK
  * preparing 'foo':
  * checking DESCRIPTION meta-information ... OK
  * installing the package to process help pages
  * saving partial Rd database
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building 'foo_1.0.tar.gz'
  
  dratting
  Error in loadNamespace(x) : there is no package called 'git2r'
  Calls: runTest ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'htmltools', 'magrittr', 'glue', 'bsplus', 'shiny', 'stringr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ROCR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'psych', 'magrittr', 'moments', 'readxl', 'shiny',
  'shinycssloaders', 'shinydashboard', 'xlsx', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pracma', 'RConics', 'rmutil', 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'ade4', 'coda', 'sde'

Packages suggested but not available for checking:
  'fda', 'ggplot2', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'gtools', 'multcomp', 'plotrix', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'trust', 'BMisc'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Formula'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'msgps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'drc', 'reshape2', 'qcc', 'odbc', 'DBI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fastDummies', 'Rcpp', 'transport', 'RcppEigen'

Package suggested but not available for checking: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nleqslv', 'Rcpp', 'data.table', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maptools', 'PBSmapping', 'raster', 'sp', 'spatstat.geom',
  'spatstat.core', 'spatstat.linnet', 'spatstat', 'spdep'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'learnr', 'gapminder', 'scales', 'gt', 'modelsummary', 'dotwhisker',
  'interplot', 'likert', 'ggthemes', 'ggeffects', 'summarytools',
  'knitr', 'tidyverse', 'car', 'arm', 'ordinal', 'moments', 'tibble',
  'performance', 'kableExtra'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'xts', 'zoo', 'RcppArmadillo'

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', 'dplyr', 'tidyr', 'ingredients'

Packages suggested but not available for checking: 'testthat', 'ranger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'seqinr', 'Biostrings', 'testthat', 'ggplot2', 'future',
  'doParallel', 'foreach', 'tidyverse', 'dplyr', 'reshape2', 'Rdpack'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'roxygen2', 'irlba'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'qusage'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sampling', 'rmarkdown', 'SmartEDA', 'data.table', 'caTools',
  'ParamHelpers', 'mlr', 'ggplot2', 'iml'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ranger', 'glmnet', 'randomForest', 'xgboost',
  'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'randomForest', 'GenomicRanges', 'GenomeInfoDb',
  'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'S4Vectors',
  'org.Hs.eg.db', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cdfDRM: no visible global function definition for 'tail'
densityDRM: no visible binding for global variable 'density'
drmdel: no visible binding for global variable 'optim'
drmdel: no visible global function definition for 'pchisq'
quantEst: no visible global function definition for 'tail'
quantileCompWald: no visible global function definition for 'pchisq'
quantileCompWald: no visible global function definition for 'p.adjust'
quantileDRM: no visible global function definition for 'tail'
quantileDRM: no visible global function definition for 'density'
Undefined global functions or variables:
  density optim p.adjust pchisq tail
Consider adding
  importFrom("stats", "density", "optim", "p.adjust", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages required but not available:
  'limma', 'DESeq2', 'SummarizedExperiment', 'ggplot2'

Packages suggested but not available for checking:
  'shiny', 'shinyBS', 'shinyjs', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'VGAM', 'ordinal', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggsci'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'copula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'kernlab', 'CVST'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SuperLearner', 'np', 'future', 'doFuture', 'future.apply',
  'future.batchtools'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'gam', 'earth', 'quadprog',
  'nloptr', 'foreach', 'stringi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ROCR', 'MESS', 'cclust', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'audio', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'unikn'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'lhs', 'nloptr', 'plotly', 'rlang', 'XML'

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'pkgdown', 'rmarkdown', 'roxygen2',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'adaptivetau', 'deSolve', 'dplyr', 'ggplot2', 'gridExtra',
  'lhs', 'nloptr', 'plotly', 'rlang', 'XML'

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'pkgdown', 'rmarkdown', 'roxygen2',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Packages required but not available:
  'ggplot2', 'xts', 'zoo', 'R2HTML', 'xtable', 'tsoutliers',
  'htmlwidgets', 'forecast', 'rJava', 'timeDate', 'dygraphs',
  'extrafont', 'gridExtra', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BB'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'limma', 'mclust'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'Rcpp', 'stringr', 'tidyr', 'tidyselect', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'knitr', 'lme4', 'rmarkdown', 'sirt',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tfplot', 'tframe', 'setRNG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dssd', 'mrds', 'Distance', 'sf', 'sp', 'ggplot2', 'rgeos',
  'rstudioapi', 'gridExtra', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'pbapply', 'knitr', 'lwgeom', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'progress', 'R6'

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:
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  'magrittr', 'testthat', 'wordcloud2', 'forcats', 'viridis'

VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 149 marked UTF-8 strings
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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ggplot2', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DSI', 'R6'

Packages suggested but not available for checking:
  'resourcer', 'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'hive'
Unavailable namespace imported from by a ':::' call: 'hive'
  See the note in ?`:::` about the use of this operator.
Packages required but not available: 'Rcpp', 'stringr'

Packages suggested but not available for checking:
  'covr', 'testthat', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DSI', 'MolgenisAuth', 'httr', 'stringr', 'base64enc', 'urltools'

Packages suggested but not available for checking:
  'dsBaseClient', 'knitr', 'mockery', 'testthat', 'tibble',
  'rmarkdown', 'metafor'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mrds', 'numDeriv', 'ggplot2', 'plyr', 'statmod'

Packages suggested but not available for checking:
  'Distance', 'sp', 'tweedie', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'opalr', 'DSI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'purrr', 'httr', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exactci', 'asht', 'loglognorm'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'stringr', 'dplyr', 'purrr', 'glue', 'tidyr', 'lubridate',
  'rlang'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'plot3D', 'rgdal'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tibble', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
  'testthat', 'pbapply', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
  'ggplot2', 'plotly', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DEoptim', 'RWiener', 'rtdists', 'ggplot2', 'Rcpp', 'RcppArmadillo'

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:
  'testthat', 'knitr', 'rmarkdown', 'igraph'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'pec', 'Ecdat', 'rpart.plot', 'Rcpp'

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 required but not available: 'igraph', 'ppcor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'matrixStats', 'FNN', 'mixtools', 'BayesTree', 'gss',
  'e1071', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DEoptimR'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 1 marked Latin-1 string
Packages required but not available:
  'km.ci', 'pomp', 'Hmisc', 'data.table', 'dplyr', 'r2d3', 'shiny',
  'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'latticeExtra', 'widgetframe', 'tidyr',
  'RColorBrewer'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gee', 'PropCIs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doParallel', 'foreach', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'checkmate', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'microbenchmark'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Distance-to-default.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'awsMethods', 'adimpro', 'aws', 'rgl', 'oro.nifti', 'oro.dicom',
  'gsl', 'quadprog'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
DTK.plot: no visible global function definition for 'axis'
DTK.plot: no visible global function definition for 'title'
DTK.plot: no visible global function definition for 'lines'
DTK.plot: no visible global function definition for 'points'
DTK.test: no visible binding for global variable 'sd'
DTK.test: no visible global function definition for 'qtukey'
TK.test: no visible global function definition for 'TukeyHSD'
TK.test: no visible global function definition for 'aov'
Undefined global functions or variables:
  TukeyHSD aov axis lines points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'diagram', 'dfcrm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'data.table', 'dplyr', 'ellipsis', 'glue', 'lifecycle',
  'rlang', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'bench', 'covr', 'knitr', 'rmarkdown', 'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'gtools', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'htmlwidgets', 'jsonlite', 'magrittr', 'crosstalk',
  'promises'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shiny', 'bslib', 'testit'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'party', 'evtree', 'partykit', 'caret'

Packages suggested but not available for checking:
  'randomForest', 'tree', 'ISLR', 'matrixStats', 'plyr', 'rpart.utils',
  'stringr', 'pROC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'kernlab', 'foreach', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'aod'

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.
Packages required but not available: 'checkmate', 'data.table', 'R6'

Packages suggested but not available for checking:
  'covr', 'dygraphs', 'fasttime', 'knitr', 'magrittr', 'RColorBrewer',
  'rmarkdown', 'runner', 'tinytest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'chk', 'hms', 'lifecycle'

Packages suggested but not available for checking:
  'covr', 'rlang', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dtw', 'rlist', 'e1071', 'entropy', 'lsa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'proxy', 'dtw', 'bigmemory', 'clue', 'dplyr', 'flexclust', 'foreach',
  'ggplot2', 'ggrepel', 'nloptr', 'RSpectra', 'Rcpp', 'RcppParallel',
  'reshape2', 'shiny', 'shinyjs', 'RcppArmadillo', 'RcppThread'

Packages suggested but not available for checking:
  'doParallel', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/dtwclust.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'proxy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'raster', 'snow', 'ggplot2', 'rgdal', 'dtw', 'proxy',
  'scales', 'reshape2', 'RColorBrewer', 'plyr', 'sp', 'lubridate',
  'caret', 'xtable', 'Rdpack', 'data.table'

Packages suggested but not available for checking:
  'gridExtra', 'png', 'Hmisc', 'rbenchmark'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dtw', 'rlist', 'e1071', 'entropy', 'lsa', 'DTWBI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'haven', 'readxl', 'readr', 'digest', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
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:
  'BiocManager', 'tibble', 'matrixcalc', 'Rfast', 'flashClust', 'RANN',
  'HiClimR', 'qlcMatrix', 'irlba', 'igraph', 'reshape2', 'FNN',
  'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DBI'

Packages suggested but not available for checking:
  'callr', 'DBItest', 'dbplyr', 'nycflights13', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crul', 'jsonlite'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tidyverse', 'ggplot2', 'rlang', 'data.table',
  'rstatix'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
dummy: no visible global function definition for 'model.matrix'
dummy: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
Packages required but not available: 'stringi', 'crayon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tibble', 'magrittr', 'stringdist', 'lintr',
  'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'numDeriv', 'nloptr', 'data.table', 'mvtnorm'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/whatmph.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'shiny', 'DT', 'reshape2'

Packages suggested but not available for checking: 'knitr', 'bs4Dash'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/DVHmetrics.Rnw'
   'inst/doc/DVHshiny.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pedtools', 'forrel', 'pedprobr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rbenchmark', 'dplyr', 'cubature', 'data.table', 'ggplot2',
  'mvtnorm', 'pracma', 'Rcpp', 'survey', 'tab'

Packages suggested but not available for checking:
  'knitr', 'microbenchmark', 'printr', 'rmarkdown', 'RcppRoll'

VignetteBuilder package required for checking but not installed: 'knitr'

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.
Packages required but not available:
  'dygraphs', 'htmltools', 'ncdf4', 'raster', 'rgdal'

Packages suggested but not available for checking:
  'hydroGOF', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'SparseM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'raster', 'berryFunctions', 'R.utils'
'LazyData' is specified without a 'data' directory
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: 'glmnet', 'hglasso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maxLik', 'DiscreteWeibull', 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CholWishart', 'RcppZiggurat', 'Rfast', 'mvtnorm'

Package suggested but not available for checking: 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ncdf4', 'tidyr', 'hydroGOF', 'ggplot2', 'RColorBrewer',
  'lubridate', 'R.utils'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Chaos01'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'htmlwidgets', 'htmltools', 'zoo', 'xts'

Package suggested but not available for checking: 'testthat'

Packages which this enhances but not available for checking:
  'rmarkdown', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'quadprog'
Package suggested but not available for checking: 'testthat'
Package unavailable to check Rd xrefs: 'stringdist'
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: 'lmtest'

Packages suggested but not available for checking:
  'urca', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'lhs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'timereg', 'captioner', 'biglm',
  'httr', 'shiny', 'formatR', 'R.rsp', 'speedglm', 'dichromat',
  'colorspace', 'plyr', 'gsl', 'mvtnorm', 'nloptr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/ddhazard.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rlang'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'knitr'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pbapply', 'seewave', 'tuneR', 'png', 'NatureSounds', 'ggplot2',
  'viridis', 'scales', 'av', 'ari', 'gganimate', 'magrittr'

Packages suggested but not available for checking: 'imager', 'fs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'maptools', 'rgdal', 'rgeos', 'zoo', 'xts', 'sp',
  'raster', 'lubridate', 'topmodel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'akima', 'tgp', 'plgp'
Running examples in 'dynaTree-Ex.R' failed
The error most likely occurred in:

> ### Name: sens.dynaTree
> ### Title: Monte Carlo Sensitivity Analysis for dynaTree Models
> ### Aliases: sens.dynaTree
> ### Keywords: methods htest
> 
> ### ** Examples
> 
> ## friedman data
> library(tgp)
Error in library(tgp) : there is no package called 'tgp'
Execution halted
Package required but not available: 'tcltk2'

Packages suggested but not available for checking: 'tkrplot', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for 'pchisq'
RunClustering : CheckClusterNew: no visible global function definition
  for 'qchisq'
RunClustering: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'var'
RunDenoising: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'median'
RunDenoising: no visible global function definition for 'var'
RunDenoising : buildEstimate: no visible global function definition for
  'qchisq'
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
Packages required but not available: 'igraph', 'Rcpp', 'Rdpack'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'zoo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpridge'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dynutils', 'irlba', 'lmds', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'diffusionMap', 'fastICA', 'igraph', 'lle', 'RANN',
  'Rtsne', 'smacof', 'uwot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'doParallel', 'foreach'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'dynutils', 'ggplot2', 'ggraph', 'ggrepel',
  'GillespieSSA2', 'igraph', 'lmds', 'patchwork', 'pbapply', 'purrr',
  'rlang', 'tibble', 'tidygraph', 'tidyr', 'viridis'

Packages suggested but not available for checking:
  'anndata', 'covr', 'dynwrap', 'R.rsp', 'rmarkdown', 'Seurat',
  'SingleCellExperiment', 'SummarizedExperiment', 'testthat'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GetIntMod: no visible global function definition for 'arima'
GetLikeDI: no visible global function definition for 'arima'
GetLikeDI: no visible global function definition for 'logLik'
GetPV: no visible global function definition for 'optimize'
GetPV: no visible global function definition for 'pchisq'
fitdi: no visible global function definition for 'optimize'
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
Packages required but not available: 'zoo', 'car', 'lmtest'

Packages suggested but not available for checking:
  'sandwich', 'strucchange', 'TSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'zoo', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'shiny', 'ggplot2', 'plotly', 'stargazer', 'prediction',
  'rms', 'dplyr', 'compare', 'BBmisc'

Package suggested but not available for checking: 'gam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'carrier', 'dplyr', 'dynutils', 'magrittr', 'purrr',
  'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'lhs', 'ParamHelpers', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mstate'
Package required but not available: 'rlang'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'corrplot', 'RColorBrewer', 'ggplot2', 'reshape2', 'vegan', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'zoo'

Packages suggested but not available for checking:
  'MCMCpack', 'quantreg', 'randomForest', 'sandwich', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'numDeriv', 'xtable', 'latex2exp', 'reshape2', 'plyr',
  'mice', 'magrittr', 'Rdpack', 'fda', 'car', 'stringi', 'tibble',
  'deSolve'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'riverplot', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gridExtra'

Packages suggested but not available for checking: 'DataCombine', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/dynsim-overview.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'ggplot2', 'nleqslv', 'splines2', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modelObj', 'kernlab', 'rgenoud', 'dfoptim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'crayon', 'desc', 'dplyr', 'magrittr', 'proxyC',
  'purrr', 'Rcpp', 'remotes', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'hdf5r', 'knitr', 'readr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'babelwhale', 'crayon', 'dplyr', 'dynutils',
  'dynparam', 'igraph', 'glue', 'magrittr', 'purrr', 'processx',
  'readr', 'stringr', 'reshape2', 'tibble', 'tidyr', 'yaml'

Packages suggested but not available for checking:
  'dyndimred', 'hdf5r', 'knitr', 'pkgload', 'ranger', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TraMineR'

Package suggested but not available for checking: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 9 marked UTF-8 strings
Packages required but not available:
  'DysPIAData', 'Rcpp', 'BiocParallel', 'fastmatch', 'data.table',
  'parmigene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'proxy'

Packages suggested but not available for checking:
  'mlbench', 'randomForest', 'SparseM', 'xtable', 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BBmisc', 'DataCombine', 'signal', 'anytime', 'chron', 'data.table',
  'ggplot2', 'scales', 'accelerometry', 'hms', 'doParallel', 'doSNOW',
  'foreach'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'modeltools', 'Rdpack'

Packages suggested but not available for checking:
  'testthat', 'withr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shinyFiles', 'shinyBS', 'ggplot2', 'ggthemes', 'plotly', 'R.utils',
  'mmap', 'matrixcalc', 'shiny', 'shinythemes', 'shinyjs',
  'data.table', 'RcppEigen', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'msm', 'mvtnorm', 'limSolve', 'hdi', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'DT', 'energyr', 'googleVis', 'leaflet', 'plotly', 'shiny',
  'shinydashboard', 'shinytest', 'shinyWidgets'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doParallel', 'betareg', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'distcrete', 'EpiEstim', 'epitrix', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'roxygen2', 'incidence', 'knitr', 'rmarkdown',
  'projections', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'moments', 'tgp', 'tseries', 'fields', 'nortest',
  'quadprog', 'Kendall', 'lmtest', 'som', 'spam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'plotmo', 'TeachingDemos'

Packages suggested but not available for checking: 'gam', 'mda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'R6', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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', 'knitr', 'rmarkdown', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abc', 'pls', 'mnormt', 'lhs', 'tensorA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'purrr', 'tidyr', 'dplyr', 'forcats', 'ggalluvial', 'ggplot2',
  'ggridges', 'RColorBrewer', 'recipes', 'rlang', 'stringr',
  'magrittr', 'tibble', 'gridExtra', 'randomForest', 'progressr',
  'progress'

Packages suggested but not available for checking:
  'testthat', 'covr', 'ISLR', 'nycflights13', 'vdiffr', 'parcats',
  'pkgdown', 'mlbench', 'earth', 'workflows', 'future', 'furrr',
  'e1071', 'caret', 'parsnip', 'vip', 'glmnet', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ca', 'vegan', 'ellipse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'multiCA', 'CATT', 'gmodels', 'psych', 'rcompanion', 'FSA', 'trend'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'PMCMRplus', 'multcomp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'markdown', 'knitr', 'ggplot2', 'scales', 'xtable',
  'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

Package suggested but not available for checking: 'rpf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ncdf4', 'ClimProjDiags', 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'devtools'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pwr'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', 'LaF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'data.table', 'digest', 'dplyr', 'glue', 'Hmisc', 'lubridate',
  'stringr', 'openssl', 'readxl', 'rlang', 'rprojroot', 'XML'

Packages suggested but not available for checking:
  'pdftools', 'qs', 'rstudioapi', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SSBtools', 'sdcTable', 'shiny'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'RegSDC', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'SpecsVerification', 'pbapply', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'R.rsp', 'verification'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rglpk', 'lpSolve'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'readxl', 'Rsymphony'

Package which this enhances but not available for checking: 'gurobi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DBI', 'RSQLite'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'eatDB', 'haven', 'plyr', 'eatTools', 'tibble', 'data.table', 'hms'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'conflicted', 'knitr', 'ggplot2', 'ggparty', 'partykit',
  'ggrepel', 'Rdpack', 'lpSolveAPI', 'reshape2'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'kableExtra', 'usethis', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'survey', 'BIFIEsurvey', 'progress', 'lavaan', 'Hmisc', 'fmsb',
  'mice', 'car', 'reshape2', 'plyr', 'combinat', 'miceadds', 'tidyr',
  'EffectLiteR', 'estimatr', 'eatTools', 'eatGADS', 'janitor', 'msm',
  'lme4'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
eb: no visible global function definition for 'optimize'
ebalance: no visible global function definition for 'var'
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
Package required but not available: 'psychotools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'wavethresh'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'GeneNet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'glmnet'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'car', 'data.table', 'dplyr', 'ggplot2', 'gridExtra', 'magrittr',
  'PresenceAbsence', 'rappdirs', 'raster', 'rlang', 'sf', 'stringr',
  'tidyr', 'viridisLite', 'xml2'

Packages suggested but not available for checking:
  'covr', 'fields', 'knitr', 'rmarkdown', 'rnaturalearth', 'smoothr',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'plyr', 'separationplot', 'Hmisc', 'abind', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mstate', 'Rcpp', 'HDInterval'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ROCR', 'BEDMatrix', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lars', 'Rdpack'

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: 'Brobdingnag', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ebSNP: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'magrittr', 'drc'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'ggridges', 'cowplot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quadprog', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'INLA'
Packages required but not available: 'curl', 'rsdmx', 'xml2', 'httr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'lubridate', 'ggplot2', 'testthat',
  'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', 'rjson', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Ecfun'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rmpfr', 'gsl', 'RcppFaddeeva', 'polynom', 'xts', 'zoo', 'optimx',
  'moments', 'stabledist', 'ggplot2', 'gridExtra', 'xtable', 'yaml',
  'RSQLite', 'digest'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'roxygen2', 'ghyp', 'fOptions', 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.core'

Package suggested but not available for checking: 'dixon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fda', 'RCurl', 'XML', 'tis', 'jpeg', 'TeachingDemos', 'stringi',
  'xml2', 'BMA', 'mvtnorm'

Packages suggested but not available for checking:
  'car', 'DescTools', 'Ecdat', 'maps', 'gridBase', 'pryr', 'knitr',
  'rmarkdown', 'invgamma', 'ipumsr', 'lubridate', 'bayesplot', 'bssm',
  'ggplot2', 'tibble', 'kableExtra', 'openxlsx', 'fitdistrplus',
  'purrr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'orthopolynom', 'bootstrap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'jsonlite'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'magrittr', 'dplyr', 'purrr', 'countrycode', 'broom',
  'shiny', 'scales', 'corrplot', 'htmltools', 'jsonlite', 'rstudioapi'

Packages suggested but not available for checking:
  'tidyr', 'testthat', 'knitr', 'rmarkdown', 'covr', 'data.tree',
  'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'htmltools', 'dplyr', 'magrittr', 'shiny', 'purrr',
  'jsonlite', 'crosstalk'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'sf', 'spData'
Running examples in 'echelon-Ex.R' failed
The error most likely occurred in:

> ### Name: echebin
> ### Title: Echelon spatial scan statistic based on Binomial model
> ### Aliases: echebin
> ### Keywords: echelon analysis spatial scan statistic spatial cluster
> ###   deteciotn
> 
> ### ** Examples
> 
> ##Hotspot detection for non-white birth of North Carolina using echelon scan
> 
> #Non-white birth from 1974 to 1984 (case data)
> library(spData)
Error in library(spData) : there is no package called 'spData'
Execution halted
Packages required but not available: 'plot3D', 'animation'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'minpack.lm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geosphere', 'readHAC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geojsonsf', 'httr', 'plyr', 'purrr', 'readr', 'rlang',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'ggspatial', 'here', 'httptest', 'kableExtra',
  'knitr', 'raster', 'rmarkdown', 'sf', 'testthat', 'utf8'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'janitor', 'labelled', 'laeken', 'purrr', 'readxl', 'rlang', 'srvyr',
  'statar', 'stringr', 'survey', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CHNOSZ'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'softImpute'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'data.table', 'dynamicTreeCut', 'magrittr', 'pacman',
  'WGCNA', 'stringr', 'pander'

Packages suggested but not available for checking:
  'earth', 'ncvreg', 'knitr', 'rmarkdown', 'protoclust', 'factoextra',
  'ComplexHeatmap', 'circlize', 'pheatmap', 'viridis', 'pROC', 'glmnet'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'sandwich', 'lmtest', 'urca', 'earth'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'keyring', 'memoise', 'getPass', 'curl'

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat', 'raster', 'maps', 'ncdf4', 'knitr',
  'rlang', 'rstudioapi', 'jsonlite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'rgeos', 'readr', 'rgdal', 'curl', 'gdalUtils', 'ggplot2',
  'rvest', 'landscapemetrics', 'sp', 'tibble', 'xml2', 'dplyr', 'sf',
  'R.utils', 'httr', 'getPass', 'rasterVis', 'viridis', 'rlang',
  'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvabund', 'glasso', 'plyr', 'sna', 'tweedie', 'igraph', 'betareg',
  'doParallel', 'glm2', 'ordinal', 'foreach'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tidyr', 'ggplot2', 'RColorBrewer',
  'ggraph', 'labdsv', 'tidygraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rjags', 'coda'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'testthat', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'operators', 'topmodel', 'DEoptim', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rgeos'

Packages suggested but not available for checking:
  'vegan', 'shape', 'Rarity', 'splancs', 'plotrix', 'FD', 'picante',
  'sp', 'geoR', 'raster', 'alphahull', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rootSolve', 'shape', 'diagram', 'deSolve'

Packages suggested but not available for checking:
  'maps', 'seacarb', 'scatterplot3d', 'deldir'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'abc', 'ggplot2'

Packages suggested but not available for checking:
  'ape', 'changepoint', 'knitr', 'picante', 'rmarkdown', 'testthat',
  'untb', 'vegan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'FNN', 'igraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'igraph', 'ggplot2'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'covr', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bbmle', 'igraph', 'intergraph', 'formula.tools', 'minpack.lm',
  'sna', 'spatstat.utils', 'plyr', 'dplyr', 'doParallel', 'progressr',
  'foreach'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'rdiversity', 'Matrix.utils', 'blockmodels', 'bipartite',
  'Rcpp', 'RcppEigen', 'RcppGSL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'Rdpack'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown', 'ggraph'

VignetteBuilder package required for checking but not installed: 'knitr'

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: 'deSolve', 'stoichcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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  'knitr', 'rmarkdown', 'testthat', 'covr', 'slam'

VignetteBuilder package required for checking but not installed: 'knitr'
GNU make is a SystemRequirements.
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: 'FD'

Packages suggested but not available for checking:
  'vegan', 'knitr', 'rmarkdown', 'data.table'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'ape', 'gbm', 'sp', 'adehabitatHR', 'adehabitatMA',
  'biomod2', 'dismo', 'ecodist', 'maptools', 'randomForest', 'raster',
  'rms', 'gtools', 'PresenceAbsence', 'doParallel', 'foreach',
  'iterators', 'classInt', 'vegan', 'poibin', 'snowfall',
  'matrixStats', 'maps', 'ks', 'nabor'

Packages suggested but not available for checking:
  'rgdal', 'rJava', 'XML', 'knitr', 'alphahull', 'rgeos', 'igraph',
  'markdown', 'dplyr', 'rmarkdown', 'qpdf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GET', 'mvtnorm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colorspace', 'corrplot', 'e1071', 'ggplot2', 'qgraph', 'igraph',
  'philentropy', 'plyr', 'purrr', 'reshape', 'rlang', 'Rmisc', 'vegan',
  'vegclust', 'withr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'bookdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'covr', 'data.table', 'dplyr', 'ggplot2', 'Hmisc', 'openxlsx',
  'readr', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'utility', 'rivernet', 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BBmisc', 'smoof', 'ParamHelpers', 'checkmate', 'parallelMap',
  'reshape2', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'urca', 'forecast', 'vars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat', 'magrittr', 'caret', 'dplyr', 'e1071',
  'pbapply', 'kernlab', 'transport'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'dae', 'emmeans', 'ggplot2', 'lme4', 'magrittr', 'pbkrtest',
  '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: 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'spdep', 'sf', 'stringr', 'tidyselect', 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'openxlsx', 'scales', 'stringr', 'tidyselect'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'rgdal'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'sf', 'sp', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bupaR', 'dplyr', 'data.table', 'ggplot2', 'ggthemes', 'glue',
  'tibble', 'shiny', 'miniUI', 'tidyr', 'shinyTime', 'lubridate',
  'purrr', 'stringr', 'rlang', 'zoo', 'hms', 'forcats'

Packages suggested but not available for checking:
  'knitr', 'eventdataR', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rJava', 'rjson', 'rJython'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lpSolve', 'geometry', 'vertexenum'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'R.utils', 'tm', 'XML', 'stringr', 'stringi', 'qdapRegex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xml2', 'httr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'lintr', 'purrr', 'rmarkdown',
  'httptest', 'tokenizers', 'devtools', 'dplyr', 'tidyr', 'roxygen2',
  'pkgdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'rjson', 'igraph', 'shiny'

Packages suggested but not available for checking: 'knitr', 'huge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'edgeR', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'jjb', 'reshape2', 'RcppArmadillo', 'rgen'

Package suggested but not available for checking: 'simcdm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'corpcor'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'miniUI', 'rstudioapi', 'DT', 'tibble', 'dplyr', 'rio',
  'magrittr', 'shinyWidgets', 'openxlsx'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'editrules', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'lpSolveAPI'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotfunctions', 'data.table'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'zoo', 'xts', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'energy', 'dHSIC', 'rBayesianOptimization'

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: 'T2EQ'
Packages required but not available:
  'distr', 'igraph', 'ellipsis', 'simpleboot', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ABCanalysis', 'AdaptGauss', 'DistributionOptimization', 'ClusterR',
  'DataVisualizations', 'ggplot2', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'mvtnorm', 'lasso2'

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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'lfactors', 'data.table', 'Formula', 'glm2', 'haven', 'LaF',
  'lme4', 'NAEPprimer', 'quantreg', 'readxl', 'tibble', 'wCorr',
  'WeMix', 'xtable'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'testthat', 'withr', 'rmarkdown', 'RColorBrewer'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ineq', 'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'tibble', 'broom', 'cli', 'withr', 'glue'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'shiny', 'ggplot2', 'ggthemes', 'magrittr', 'rgeos',
  'plotly', 'sp', 'tidyr', 'purrr', 'colourpicker', 'rgdal', 'stringi',
  'tibble', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'maptools', 'purrrlyr', 'GGally',
  'corrplot', 'broom', 'scales', 'readr', 'gridExtra', 'tidyverse',
  'spelling', 'ggmap'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'mvtnorm', 'rstanarm', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
geteegdata: no visible global function definition for 'untar'
geteegdata: no visible global function definition for 'read.table'
geteegdata: no visible global function definition for 'write.csv'
geteegdata: no visible global function definition for 'write.table'
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'eegkitdata', 'bigsplines', 'ica', 'rgl', 'signal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'emplik', 'rootSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'nnfor', 'Rlibeemd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'Rlibeemd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'colorRamps', 'R.utils', 'sp', 'ggplot2'

Packages suggested but not available for checking:
  'pls', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'dplyr', 'R.matlab', 'pracma', 'rlist', 'viridis',
  'purrr', 'assertthat'

Packages suggested but not available for checking:
  'cdom', 'magrittr', 'testthat', 'knitr', 'rmarkdown', 'ggplot2',
  'plot3D', 'extrafont', 'tidyr', 'shiny', 'DT', 'MBA'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'arm', 'data.table', 'vcd', 'maptools'

Packages suggested but not available for checking:
  'testthat', 'stringr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'viridis'

Packages suggested but not available for checking:
  'dlnm', 'ggplot2', 'gridExtra', 'knitr', 'rmarkdown', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'psych', 'polycor', 'EFAtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'optimbase', 'psych', 'scales', 'PCovR', 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lavaan', 'psych', 'crayon', 'stringr', 'ggplot2', 'tibble',
  'magrittr', 'dplyr', 'cli', 'Rcpp', 'viridisLite', 'future.apply',
  'future', 'GPArotation', 'checkmate', 'tidyr', 'progressr',
  'progress', 'rlang', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'microbenchmark'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GPArotation', 'plyr', 'mvtnorm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'copula', 'foreach', 'doParallel', 'waveslim', 'gstat', 'tidyr',
  'dplyr', 'sp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'ggplot2', 'RCurl', 'fields',
  'gridExtra', 'animation'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lavaan', 'shiny', 'ggplot2', 'survey', 'lavaan.survey', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'seqinr', 'ggplot2', 'shiny', 'reshape2', 'rmarkdown', 'viridis'

Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bayestestR', 'insight', 'parameters'

Packages suggested but not available for checking:
  'correlation', 'covr', 'dplyr', 'gamm4', 'ggplot2', 'knitr', 'lme4',
  'lmerTest', 'modelbased', 'performance', 'rmarkdown', 'rstanarm',
  'rstantools', 'see', 'spelling', 'testthat', 'tidyr'

Packages which this enhances but not available for checking:
  'afex', 'BayesFactor', 'brms', 'car', 'emmeans', 'lavaan', 'lm.beta',
  'mediation', 'MuMIn', 'pscl', 'tidymodels'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Kendall'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'carData', 'lme4', 'colorspace', 'survey', 'estimability', 'insight'

Packages suggested but not available for checking:
  'pbkrtest', 'poLCA', 'heplots', 'ordinal', 'car', 'knitr', 'betareg',
  'alr4', 'robustlmm'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/methods-supported-by-effects.Rnw'
   'inst/doc/partial-residuals.Rnw'
   'inst/doc/predictor-effects-gallery.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Package unavailable to check Rd xrefs: 'PsumtSim'
Packages required but not available: 'VGAM', 'miscTools'

Packages suggested but not available for checking:
  'DIFlasso', 'DIFboost', 'VGAMdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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
Packages required but not available: 'zoo', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'covr', 'sandwich', 'tibble', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'TMB', 'dplyr', 'RcppEigen'

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', 'ensurer', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jsonlite', 'httr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'party', 'pROC', 'randomForest', 'ROCR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'lubridate', 'magrittr', 'xts', 'plyr', 'ncdf4',
  'udunits2'

Packages suggested but not available for checking:
  'testthat', 'zoo', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qgraph', 'semPlot', 'igraph', 'lavaan', 'NetworkToolbox', 'glasso',
  'dplyr', 'network', 'GGally'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'kableExtra', 'psych',
  'psychTools', 'ggpubr', 'ggplot2', 'tidyselect', 'corpcor', 'plyr',
  'matrixcalc', 'pbapply', 'OpenMx', 'wTO', 'fitdistrplus', 'primes',
  'purrr', 'shiny', 'shinyjs', 'shinyalert', 'shinyBS', 'R.matlab',
  'readxl', 'gridExtra', 'rstudioapi', 'RColorBrewer', 'infutil'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'xts', 'ggplot2', 'tseries', 'urca', 'pracma', 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'coda', 'numbers', 'rootSolve', 'BH', 'StanHeaders',
  'RcppEigen'

Packages suggested but not available for checking:
  'eggCountsExtra', 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gridExtra', 'ggplot2', 'gtable'

Packages suggested but not available for checking: 'knitr', 'png'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidygraph', 'srvyr', 'tidyr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'survey', 'shiny', 'igraph',
  'network', 'haven'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EGRET', 'binom'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'doParallel', 'iterators', 'rmarkdown',
  'pkgdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dataRetrieval', 'fields', 'truncnorm', 'foreach'

Packages suggested but not available for checking:
  'EGRETci', 'knitr', 'rmarkdown', 'extrafont', 'testthat', 'rkt',
  'doParallel', 'pkgdown', 'png', 'dplyr', 'zyp', 'lubridate', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'purrr', 'mvtnorm', 'matrixStats'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Errors in running code in vignettes:
when running code in 'parametric1.Rnw'
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'parametric1.Rnw' using 'UTF-8'... failed to complete the test
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'crayon'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running examples in 'ehelp-Ex.R' failed
The error most likely occurred in:

> ### Name: ehelp
> ### Title: Enhanced-Help Function: ehelp() This function displays docstring
> ###   style comments used as help liners for user defined functions.
> ### Aliases: ehelp
> ### Keywords: internal
> 
> ### ** Examples
> 
> myTestFn <- function(x,y,z,t=0) {
+ #'
+ #' This is just an example of a dummy fn
+ #'
+ #'
+ #' @email myemail@somewhere.org
+ #' @author author
+ #
+ #
+ #' @demo
+ #' @examples myTestFn(x0,y0,z0)
+ }
> 
> ehelp(myTestFn)
Error in loadNamespace(x) : there is no package called 'crayon'
Calls: ehelp ... 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
Skipping vignette re-building
Packages suggested but not available for checking:
  'vegdata', 'vegan', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/eHOF.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/eHOF.Rnw'
(Is a VignetteBuilder field missing?)
Package required but not available: 'data.table'

Packages suggested but not available for checking:
  'glmnet', 'logistf', 'medExtractR', 'knitr', 'rmarkdown', 'ggplot2',
  'formula.tools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'plotly', 'zoo', 'xts', 'lubridate', 'RColorBrewer',
  'viridis', 'scales'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'BiocStyle', 'dbscan', 'webshot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'xts', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'magrittr', 'httr', 'jsonlite', 'dplyr', 'purrr',
  'memoise', 'lubridate', 'readxl'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'tidyr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GA', 'snow', 'doSNOW', 'iterators', 'pso', 'ucminf', 'foreach',
  'optimParallel'

Packages suggested but not available for checking:
  'igraph', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'eiPack', 'ei', 'wru', 'censusxy', 'bayestestR', 'coda',
  'data.table', 'doParallel', 'dplyr', 'foreach', 'ggplot2',
  'magrittr', 'mcmcse', 'overlapping', 'purrr', 'rlang', 'sf',
  'stringr', 'tidyr', 'leaflet', 'tidyselect'

Packages suggested but not available for checking:
  'knitr', 'opencage', 'plyr', 'rmarkdown', 'reshape2', 'RColorBrewer',
  'RJSONIO', 'testthat', 'tigris'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
eiginv: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for 'cov'
boot_pr_comp: no visible global function definition for 'quantile'
boot_pr_comp: no visible global function definition for 'segments'
boot_pr_comp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gridExtra'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'igraph', 'magrittr', 'shiny', 'entropy'

Packages suggested but not available for checking:
  'testthat', 'RColorBrewer', 'knitr', 'rmarkdown', 'bench'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'eiPack', 'mvtnorm', 'msm', 'tmvtnorm', 'ellipse', 'plotrix',
  'ucminf', 'cubature', 'mnormt', 'foreach', 'sp'

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'reshape2', 'optimx', 'magrittr', 'shiny', 'shinydashboard',
  'shinycssloaders', 'readxl'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'R2jags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'ncdf4', 'raster', 'sp', 'cptcity', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'covr', 'lwgeom', 'units', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'data.table', 'purrr', 'xgboost', 'DALEX', 'ggrepel',
  'ggiraphExtra', 'iBreakDown', 'tidyr', 'scales'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'lightgbm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'seriation', 'shiny', 'dplyr', 'purrr', 'rlang', 'tidyr', 'forcats',
  'RColorBrewer', 'bsplus', 'dendextend', 'haven', 'reshape2', 'shape',
  'shinyWidgets', 'shinydashboard'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'SiZer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'glmnet', 'reshape2', 'cvTools', 'qgraph'

Packages suggested but not available for checking: 'IsingSampler', 'akima'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'crul', 'jsonlite', 'R6'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

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: 'elec'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'data.table', 'haven', 'readr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.