Packages required but not available: 'robustbase', 'chipPCR'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', '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:
  'scales', 'utf8', 'formatR', 'dplyr', 'R2jags', 'rjags', 'magrittr',
  'checkmate', 'Rdpack', 'igraph', 'rgeos', 'reshape2'

Packages suggested but not available for checking:
  'overlapping', 'ggplot2', 'RColorBrewer', 'mcmcplots', 'testthat',
  'crayon', 'Hmisc', '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', 'R2jags', 'rjags', 'reshape2', 'magrittr', 'checkmate',
  'Rdpack'

Packages suggested but not available for checking:
  'knitr', 'scales', 'overlapping', 'ggplot2', 'igraph', 'rmarkdown',
  'testthat', 'RColorBrewer', 'mcmcplots'

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

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

Packages suggested but not available for checking:
  'TH.data', 'fields', 'BayesX', 'gbm', 'mlbench', 'RColorBrewer',
  'randomForest', 'testthat', 'kangar00'

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

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: 'nleqslv', 'enrichwith'

Package suggested but not available for checking: 'brglm'

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

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: 'MCMCpack', 'mnormt', 'truncnorm'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'babette', 'beautier', 'beastier', 'curl', 'devtools', 'mauricer',
  'Rmpfr', 'testit', 'txtplot'

Packages suggested but not available for checking:
  'ape', 'ggplot2', 'hunspell', 'knitr', 'lintr', 'nLTT', 'phangorn',
  'rappdirs', 'rmarkdown', 'spelling', 'stringr', 'testthat',
  'tracerer'

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:
  'leaps', 'lars', 'glmnet', 'ncvreg', 'smoothmest', 'ggplot2',
  'reshape2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'pROC', 'caret', 'rgl'

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

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.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getbetap.A: no visible global function definition for 'pbeta'
getbetap.A: no visible global function definition for 'cor.test'
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
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:
  'Rglpk', 'glpkAPI', 'RColorBrewer', 'combinat'

Packages suggested but not available for checking: 'Rgraphviz', 'cplexAPI'

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

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

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

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

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: 'randtoolbox', 'snow'

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

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

Packages suggested but not available for checking:
  'HSAUR3', 'roxygen2', 'knitr', 'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 46 marked UTF-8 strings
Packages required but not available:
  'spam', 'rsm', 'fields', 'maxLik', 'nleqslv', 'spdep'

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/mclcar_vignette.Rnw'
(Is a VignetteBuilder field missing?)

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

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

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'evir'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'chk', 'extras', 'mcmcr', 'nlist', 'purrr', 'universals'

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

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

Packages suggested but not available for checking:
  'coda', 'mockery', '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:
  'coda', 'ape', 'corpcor', 'tensorA', 'cubature'

Packages suggested but not available for checking:
  'rgl', 'combinat', 'mvtnorm', 'orthopolynom'

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

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

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

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

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

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: 'MCMCglmm', 'ggplot2', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'xtable', 'Iso'
Running 'accept-batch.R'
  Comparing 'accept-batch.Rout' to 'accept-batch.Rout.save' ... OK
  Running 'circle.R'
  Comparing 'circle.Rout' to 'circle.Rout.save' ... OK
  Running 'initseq.R'
Running the tests in 'tests/initseq.R' failed.
Last 13 lines of output:
  [1] TRUE
  > 
  >  length(out$Gamma.pos) == length(Gamma)
  [1] TRUE
  >  all.equal(out$Gamma.pos, Gamma)
  [1] TRUE
  > 
  >  Gamma.dec <- cummin(Gamma)
  >  all.equal(out$Gamma.dec, Gamma.dec)
  [1] TRUE
  >  
  > ## IGNORE_RDIFF_BEGIN
  > library(Iso)
  Error in library(Iso) : there is no package called 'Iso'
  Execution halted
Errors in running code in vignettes:
when running code in 'demo.Rnw'
  ...
> foo <- rbind(mu, mu.mcse)

> dimnames(foo) <- list(c("estimate", "MCSE"), c("constant", 
+     paste("$x_", 1:4, "$", sep = "")))

> library(xtable)

  When sourcing 'demo.R':
Error: there is no package called 'xtable'
Execution halted

  'bfst.Rnw' using 'UTF-8'... OK
  'debug.Rnw'... OK
  'demo.Rnw' using 'UTF-8'... failed
  'morph.Rnw' using 'UTF-8'... OK
Error(s) in re-building vignettes:
  ...
--- re-building 'bfst.Rnw' using Sweave
--- finished re-building 'bfst.Rnw'

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

--- re-building 'demo.Rnw' using Sweave

Error: processing vignette 'demo.Rnw' failed with diagnostics:
 chunk 19 (label = tab1) 
Error in library(xtable) : there is no package called 'xtable'

--- failed re-building 'demo.Rnw'

--- re-building 'morph.Rnw' using Sweave
Error in lud.induced(1:4) : 
  log unnormalized density function returned vector not scalar
--- finished re-building 'morph.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'abind', 'chk', 'coda', 'extras', 'generics', 'lifecycle', 'nlist',
  'purrr', 'term', 'universals'

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

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

Packages suggested but not available for checking:
  'BayesLogit', 'lintools', 'spdep', 'maptools', 'bayesplot', 'coda',
  'testthat', 'roxygen2', 'knitr', 'rmarkdown', '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: 'ellipse', 'Rcpp', 'RcppArmadillo'

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

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

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

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

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', 'rstan', 'overlapping', '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:
  'BBmisc', 'ecr', 'checkmate', 'parallelMap', 'reshape2', 'gtools',
  'vegan', 'ggplot2', 'lhs'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
do.linear.conjoint: no visible global function definition for
  'as.formula'
do.linear.conjoint: no visible global function definition for 'lm'
do.linear.conjoint: no visible global function definition for
  'coefficients'
is.close.to.orthogonal: no visible global function definition for 'cor'
mc.add.to.design: no visible global function definition for 'combn'
mc.good.designs: no visible global function definition for 'combn'
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'scatterplot3d', '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:
  'mvtnorm', 'multcomp', 'magic', 'MCMCpack', 'plyr'

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

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: 'DoseFinding'

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:
  'mvtnorm', 'shiny', 'shinydashboard', 'devEMF', 'officer',
  'flextable', 'Rcpp', 'RcppNumerical', 'RcppEigen'

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

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:
  'future', 'future.apply', 'rjags', 'coda', 'loo', 'bayesplot',
  'tidybayes', 'dplyr', 'magrittr', 'tidyr', 'tidyselect', 'tibble',
  'stringr', 'ggplot2', 'patchwork', 'rlang'

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

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

Packages suggested but not available for checking:
  'knitr', 'markdown', 'multcomp'

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

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

Package suggested but not available for checking: 'tkrplot'

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 suggested but not available for checking: 'RUnit', 'XML'
Package required but not available: 'CircStats'

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:
  'dplyr', 'ggplot2', 'ggthemes', 'gridExtra', 'magrittr', 'rlang',
  'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'testthat', 'rlang', 'Rdpack', 'simctest'

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', 'igraph', 'ggplot2', 'purrr', 'magrittr', 'reshape2',
  'shiny', 'dplyr', 'psych', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'mplot', '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:
  'logistf', 'Rcpp', 'pcalg', 'mgm', 'bnlearn', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'devtools', 'roxygen2', 'knitr', 'testthat',
  'rmarkdown', 'spelling', 'httr', 'covr', 'gh', 'rlang', 'openssl',
  'git2r', 'pkgbuild', 'curl', 'VIM', 'FactoMineR', 'mice'

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: 'earth', '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 suggested but not available for checking: 'testthat'
Packages required but not available:
  'Rdpack', 'orthopolynom', 'foreach', 'doParallel', 'ggplot2', 'psych'

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: 'readr'

Package suggested but not available for checking: 'testthat'

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

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', 'covr'

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', '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
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'testthat', 'BH', 'psqn'

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

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 suggested but not available for checking: 'RGtk2', 'coin'
'LazyData' is specified without a 'data' directory
Running examples in 'mdir.logrank-Ex.R' failed
The error most likely occurred in:

> ### Name: mdir.logrank
> ### Title: Two-sample multiple-direction log rank test
> ### Aliases: mdir.logrank
> 
> ### ** Examples
> 
> library(coin)
Error in library(coin) : there is no package called 'coin'
Execution halted
Package required but not available: 'futile.logger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RMySQL', 'shinydashboard', 'DBI', 'DT', 'leaflet', 'leaflet.extras',
  'shinyjs', 'ggplot2', 'dplyr', 'readxl', 'plotly', 'reactable',
  'writexl', 'xfun', 'berryFunctions', 'shinyWidgets', 'shiny',
  'htmltools', 'bslib', 'htmlwidgets'

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

Packages which this enhances but not available for checking:
  'JointAI', 'jomo', 'mice', 'smcfcs'

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

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:
  'reshape2', 'ggplot2', 'nloptr', 'rootSolve', 'psych', 'magic',
  'glmnet'

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', 'gplots', 'gtools'

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: 'linprog'

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: 'Sleuth3'
Running examples in 'mdscore-Ex.R' failed
The error most likely occurred in:

> ### Name: summary.mdscore
> ### Title: Summary methods for mdscore objects
> ### Aliases: summary.mdscore
> ### Keywords: mdscore score glm
> 
> ### ** Examples
> 
> library(Sleuth3)
Error in library(Sleuth3) : there is no package called 'Sleuth3'
Execution halted
Packages required but not available: 'ellipse', 'mnormt', 'polycor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'scatterplot3d', 'tcltk2', 'tkrplot', 'rpanel', 'rgl'

Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Packages suggested but not available for checking: 'qtl', '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:
  'smacof', 'clusterSim', 'symbolicDA', 'smds', 'animation', 'plotrix',
  'spdep'

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: 'shiny', 'rmarkdown', 'dplyr', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'parsedate', '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:
  'babynames', 'DBI', 'dbplyr', 'downloader', 'dplyr', 'fs', 'ggplot2',
  'htmlwidgets', 'kableExtra', 'RMySQL', 'skimr', 'stringr', 'tibble',
  'webshot'

Packages suggested but not available for checking:
  'knitr', 'Lahman', 'leaflet', 'etl', 'macleish', 'mosaic',
  'mosaicData', 'lubridate', 'sf', 'testthat', 'utf8'

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

Package suggested but not available for checking: 'glue'

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

Packages suggested but not available for checking:
  'R.rsp', 'RUnit', 'Rmosek', 'mvtnorm', 'MethylCapSig', 'gtools'

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
Packages required but not available: 'dplyr', 'tibble', '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:
  'emdist', 'ggplot2', 'gridExtra', 'reshape2', 'plyr', 'gtools',
  'Rcpp'

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:
  'assertthat', 'cli', 'httr', 'jsonlite', 'rappdirs'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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: 'pastecs', 'png', 'tiff', 'dplR'

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

Packages suggested but not available for checking:
  'car', 'ConvergenceConcepts', 'geepack', 'lmtest', 'strucchange',
  'plm', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'ellipse', 'latentnet', 'vegan', 'e1071'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'spdep', 'ggplot2', 'httr', 'jsonlite', 'meteoland', '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: 'multcomp', 'car', 'sandwich'

Packages suggested but not available for checking:
  'arm', 'gam', 'glmnet', 'mice', 'mitools', 'SuperLearner', 'VGAM'

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

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: 'Rcpp', 'RcppEigen'

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

Packages suggested but not available for checking:
  'flextable', 'knitr', 'officer', '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:
  'rvest', 'xml2', 'lubridate', 'stopwords'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'mvtnorm', 'sandwich', 'lpSolve', 'Hmisc', 'lme4'

Packages suggested but not available for checking:
  'quantreg', 'VGAM', 'SuppDists', 'testthat', 'speedglm'

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

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

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

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', 'ggplot2', 'maps', 'magrittr',
  '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:
  'audio', 'checkmate', 'deldir', 'wesanderson'

Package suggested but not available for checking: 'svglite'

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

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:
  'ggplot2', 'rgdal', 'sp', 'raster', 'rgeos', 'hms', 'tibble', 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'patchwork', 'tm', 'wordcloud2'

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: 'jmvcore', 'R6', 'lavaan', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
conf.interval: no visible global function definition for 'pbinom'
conf.statement: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'curl', 'jsonlite', 'httr', 'stringr', 'rlang', 'vroom',
  'bib2df', 'tibble', 'progress', 'lubridate', 'purrr', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'kableExtra', '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:
  'matrixStats', 'seriation', 'stringdist', 'TraMineR',
  'WeightedCluster'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'utf8'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mefa'
Package unavailable to check Rd xrefs: 'mefa'
Running 'mefa4comparisons.R'
Running the tests in 'tests/mefa4comparisons.R' failed.
Complete output:
  > ## performance comparison
  > library(mefa)
  Error in library(mefa) : there is no package called 'mefa'
  Execution halted
Packages suggested but not available for checking: 'vegan', 'mefa4'
Packages unavailable to check Rd xrefs: 'reshape', 'simba', 'labdsv', 'vegan', 'Hmisc', 'untb'
Errors in running code in vignettes:
when running code in 'mefa.Rnw'
  ...
AIC: 117.2

Number of Fisher Scoring iterations: 4


> library("vegan")

  When sourcing 'mefa.R':
Error: there is no package called 'vegan'
Execution halted

  'mefa.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'mefa.Rnw' using Sweave
mefa 3.2-7 	 2016-01-11

Error: processing vignette 'mefa.Rnw' failed with diagnostics:
 chunk 40 
Error in library("vegan") : there is no package called 'vegan'

--- failed re-building 'mefa.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'doParallel', 'foreach', 'igraph', 'Rcpp', 'ggplot2', 'reshape',
  'fpc', 'ggrepel', 'ggraph', '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: 'plyr', 'leaps'

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:
  'ggplot2', 'plyr', 'dplyr', 'reticulate', 'Rcpp', 'shiny', 'shinyjs',
  'tidyr', 'leaflet', 'tibble', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinydashboard', 'shinyWidgets', 'shinyBS',
  'shinyjs', 'RColorBrewer', 'tidyr', 'dplyr', 'openxlsx', 'haven',
  'readxl', 'stringr', 'stringi', 'DT', 'RODBC', 'formattable',
  'ggplot2', 'plotly', 'mem'

Packages suggested but not available for checking: 'magick', 'animation'

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

Packages suggested but not available for checking:
  'cowplot', 'ggimage', 'knitr', 'rmarkdown', 'prettydoc', 'shadowtext'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'showtext', 'sysfonts', 'png', 'jpeg', 'Cairo', 'ggplot2', 'cowplot',
  'magrittr', 'purrr', 'shiny', 'shinycssloaders', 'shinyBS',
  'colourpicker'

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

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

Packages suggested but not available for checking:
  'adegenet', 'geosphere', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/memgeneTutorial.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: 'repr', 'data.table'

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

Packages which this enhances but not available for checking:
  'AER', 'car', 'eha', 'lme4', 'ordinal', 'simex', 'tibble', '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:
  'urca', 'forecast', 'fracdiff', 'LongMemoryTS', 'sandwich',
  'strucchange', 'longmemo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'xts', 'zoo', '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: 'digest', 'uuid', 'magrittr'

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

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

Packages suggested but not available for checking:
  'digest', 'aws.s3', 'covr', 'googleAuthR', 'googleCloudStorageR',
  'httr', 'testthat'

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

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', 'ranger', 'cowplot', 'viridis', 'viridisLite', 'zoo',
  'stringr', 'HH', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'formatR', 'kableExtra', 'magrittr', 'knitr',
  'rmarkdown', 'rpart.plot', 'randomForest', 'virtualPollen'

VignetteBuilder 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', 'rmarkdown', 'knitr'

Packages suggested but not available for checking: 'kableExtra', '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:
  'sm', 'RColorBrewer', 'mclust', 'ggplot2', 'tidyr', 'dplyr', 'purrr',
  'RcppRoll', 'EnvStats'

Package suggested but not available for checking: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'rmarkdown', 'plotly', 'ggplot2', 'robustbase', 'iterpc',
  'quantreg', 'rjson', '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: 'plyr', 'mvtnorm', 'pracma', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Thresher', 'Rtsne', 'ClassDiscovery', 'Polychrome', 'dendextend',
  'igraph', 'flexmix'

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', 'nonnest2', 'sandwich', 'lavaan', 'numDeriv', 'lmeInfo'

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

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

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.
Packages required but not available: 'randtoolbox', 'statmod'

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:
  'arm', 'lme4', 'dplyr', 'mvtnorm', 'foreach', 'shiny', 'abind',
  'ggplot2', 'blme', 'broom.mixed'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'future.apply', 'rstanarm',
  'Amelia', 'DT'

VignetteBuilder 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', 'magrittr', 'rlang', 'stringr'

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', 'geepack', 'geeM', 'ggplot2', 'ggformula', 'glmnet',
  'kinship2', 'mvtnorm', 'RcppArmadillo'

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

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

Package suggested but not available for checking: 'INLA'

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

Package suggested but not available for checking: 'rmeta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'GenABEL'
Malformed Description field: should contain one or more complete sentences.
dometa: no visible global function definition for 'qchisq'
dometa: no visible global function definition for 'median'
dometa: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'qnorm'
forestplot: no visible global function definition for 'points'
forestplot: no visible global function definition for 'text'
metagwa.files: no visible global function definition for 'read.csv'
metagwa.files: no visible global function definition for 'write.csv'
metagwa.tables: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  median pchisq points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'bridgesampling', 'coda', 'LaplacesDemon', 'logspline',
  'mvtnorm', 'RcppParallel', 'rstan', 'rstantools', 'BH', 'RcppEigen',
  'StanHeaders'

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.
Packages required but not available:
  'mclust', 'mvtnorm', 'ellipse', 'gtools', 'gplots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'magrittr', 'usethis', 'dplyr', 'ggplot2', 'ggfittext',
  'cli', 'forcats', 'ggimage', 'patchwork', 'scales', 'stringr',
  'tidyr', 'purrr', 'meta', 'glue', 'rmarkdown'

Packages suggested but not available for checking:
  'knitr', 'here', 'Rd2roxygen', 'kableExtra', 'fansi', 'downloadthis',
  'spelling'

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

Packages suggested but not available for checking:
  'covr', 'testthat', 'tibble', '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:
  'enviPick', 'ggplot2', 'scales', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'C50', 'caret', 'e1071', 'mixOmics', 'pcaMethods', 'plyr', 'ropls',
  'rlang'

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'

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'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MLmetrics', 'xcms', 'reshape2', 'knitr', 'ggplot2', 'plotrix',
  'klaR', 'fastAdaboost', 'randomForest', 'kernlab', 'BiocStyle',
  'graph', 'Rgraphviz', 'caret'

Package suggested but not available for checking: '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:
  'taxa', 'stringr', 'ggplot2', 'igraph', 'scales', 'taxize', 'seqinr',
  'reshape2', 'zoo', 'traits', 'RColorBrewer', 'RCurl', 'ape',
  'reshape', 'lazyeval', 'dplyr', 'magrittr', 'readr', 'rlang',
  'biomformat', 'phylotate', 'ggfittext', 'vegan', 'ggrepel',
  'cowplot', 'GA', 'Rcpp', 'crayon', 'svglite', 'viridisLite', 'tibble'

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

VignetteBuilder 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', 'plyr', 'dplyr', 'data.table', 'ggplot2', 'Cairo'

Package suggested but not available for checking: 'testthat'

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.
Packages required but not available: 'rmeta', 'gsl'

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

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:
  'rvest', 'RCurl', 'XML', 'SPARQL', 'pacman', 'rcdk', 'rJava',
  'pbapply', 'enviPat', 'data.table', 'RSQLite', 'DBI', 'gsubfn',
  'stringr', 'WikidataQueryServiceR', 'webchem', 'openxlsx',
  'jsonlite', 'R.utils', 'KEGGREST', 'zip', 'ChemmineR', 'xml2',
  'stringi', 'reshape2', 'Hmisc', 'httr', 'RJSONIO', 'readxl', 'cmmr',
  'progress', 'Rdisop', 'rlist'

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

Packages suggested but not available for checking:
  'mockery', '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:
  'metadynminer', 'rgl', 'Rcpp', 'misc3d'

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'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gridExtra', 'caret', 'ggplot2', 'e1071', 'gbm', 'randomForest'

Packages suggested but not available for checking: 'knitr', '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', 'plyr', 'colorspace', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'devtools', 'TeachingDemos', 'RColorBrewer', 'reshape2'

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

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

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

Packages suggested but not available for checking:
  'testthat', 'caret', 'knitr', 'rmarkdown', '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:
  'lme4', 'numDeriv', 'minqa', 'nloptr', 'dfoptim', 'ucminf',
  'optimParallel', 'CompQuadForm', 'mvtnorm', 'BiasedUrn', 'Epi',
  'GLMMadaptive', 'multcomp', 'gsl', 'sp', 'crayon', 'R.rsp',
  'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Packages unavailable to check Rd xrefs: 'lme4', 'numDeriv', 'minqa', 'nloptr', 'dfoptim', 'ucminf', 'optimParallel'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ### to also run skip_on_cran() tests, uncomment:
  > #Sys.setenv(NOT_CRAN="true")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'glmnet', 'evd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'knitr', 'metafor', 'metap', 'purrr',
  'rlang', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'future', 'multtest', 'gamm4', 'gratia', 'roxygen2', 'rmarkdown',
  'devtools', 'covr', 'viridis', '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: 'metafor', 'stringr'

Packages suggested but not available for checking:
  'EBImage', 'ape', 'hexView', 'RCurl', 'testthat', '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:
  '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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rsolnp', 'corpcor', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BiocManager', 'rmeta', 'multtest', 'ggplot2', 'Rmisc', 'gplots',
  'Biobase', 'RMySQL', 'DBI', 'stringr', 'preprocessCore', 'GEOquery',
  'GEOmetadb', 'RSQLite', 'data.table', 'ggpubr', 'ROCR', 'zoo',
  'pracma', 'COCONUT', 'Metrics', 'manhattanly', 'DT', 'pheatmap',
  'plyr', 'dplyr', 'reshape2', 'rmarkdown', 'AnnotationDbi',
  'HGNChelper', 'magrittr', 'readr', 'plotly', 'httpuv'

Packages suggested but not available for checking:
  'BiocStyle', 'knitr', 'RUnit', 'BiocGenerics', 'snplist', 'magick'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dataone', 'dplyr', 'EML', 'emld', 'lubridate', 'purrr', 'readr',
  'stringr', 'tibble', 'tidyr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'udunits2'

VignetteBuilder 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', 'e1071', 'fgui', 'googleVis', 'maptools', 'rgeos',
  'rgrass7', 'raster', 'spatstat.geom', 'spatstat.core', 'sp',
  'minpack.lm', 'zipfR', 'coda', 'knitr'

Package suggested but not available for checking: 'rasterVis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gss', 'plyr', 'zoo', 'pracma', 'ggplot2', 'doParallel',
  'metagenomeSeq', 'DESeq2', 'edgeR'

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: 'limma', 'SMVar'

Packages suggested but not available for checking:
  'GEOquery', 'org.Hs.eg.db', 'VennDiagram', 'annaffy',
  'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'

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

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

Packages suggested but not available for checking:
  'shiny', 'miniUI', 'testthat', 'data.table', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gamlss', 'meta', 'lme4', 'gdata', 'plyr', 'dplyr', 'tidyr',
  'ggplot2', 'gridExtra', 'lmerTest', 'matrixStats', 'zCompositions',
  'compositions'

Packages suggested but not available for checking:
  'testthat', 'RCurl', 'httr', 'repmis', 'jsonlite', 'knitr',
  'rmarkdown', 'gplots', 'magrittr', 'reshape2', 'caret',
  'randomForest', 'tsibble', '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:
  'metafor', 'mvtnorm', 'lme4', 'plyr', 'pROC', 'ggplot2'

Packages suggested but not available for checking:
  'runjags', 'rjags', 'logistf', 'testthat'

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

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/guide.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'GGally', 'ggforce', 'ggplot2', 'ggrepel', 'lme4',
  'lmerTest', 'magrittr', 'mathjaxr', 'patchwork', 'purrr', 'rlang',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'DT', 'knitr', '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:
  'Rcpp', 'ggplot2', 'gridExtra', 'RcppArmadillo', 'RcppProgress', '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:
  'Biobase', 'GSEABase', 'genefilter', 'impute'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'encode', 'magrittr', 'dplyr', 'tidyr', 'rlang', 'gridExtra',
  'gtable', 'ggplot2', 'scales'

Package suggested but not available for checking: 'csv'

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:
  'knitr', '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:
  'bbmle', 'metafor', 'numDeriv', 'fastGHQuad', 'lme4'

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: 'gridBezier'

Package suggested but not available for checking: 'grImport'

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

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:
  'Rdpack', 'TFisher', 'mutoss', 'mathjaxr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'dendextend', 'dplyr', 'ggforce', 'ggrepel', 'reshape2',
  'stringr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'metafor', 'lme4', 'CompQuadForm', 'xml2'

Package suggested but not available for checking: 'BiasedUrn'

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

Packages suggested but not available for checking:
  'metafor', 'lme4', 'numDeriv', 'BiasedUrn', '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: 'rstpm2', 'mvmeta', 'meta', 'survRM2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'DESeq2', 'VennDiagram'
Packages required but not available: 'ordinal', 'maxLik', 'truncnorm'

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

Packages suggested but not available for checking:
  'metafor', 'semPlot', 'R.rsp', '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: 'meta'

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

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.
Package required but not available: 'mvtnorm'

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:
  'htmltools', 'knitr', 'magrittr', 'purrr'

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: 'lme4', 'mpt'

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

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

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

Packages suggested but not available for checking:
  'Cairo', '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:
  'metafor', 'dplyr', 'forestmodel', 'magrittr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'covr', '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: 'raster', 'sp', 'zoo', 'ncdf4', 'XML'

Packages suggested but not available for checking: 'rgdal', 'rasterVis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'spdep', 'rgdal', 'ncdf4', 'httr', 'jsonlite', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'forecast', 'spacetime', 'stars', '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', 'spacetime', 'rgdal', 'gstat', 'raster', 'snowfall', 'plyr'

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

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

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: 'statmod'

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

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

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

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

Package suggested but not available for checking: 'lme4'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
RUVRand: no visible global function definition for 'barplot'
RUVRand: no visible global function definition for 'prcomp'
RuvRandIter: no visible global function definition for 'kmeans'
RuvRandIter: no visible global function definition for 'barplot'
RuvRandIter: no visible global function definition for 'prcomp'
opt: no visible global function definition for 'optim'
printdata: no visible global function definition for 'head'
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'scales', 'stringr', 'tibble', 'lubridate', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'gplots', 'fastcluster'

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: 'DiPs'

Package suggested but not available for checking: 'optmatch'

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

Packages suggested but not available for checking:
  'testthat', 'RColorBrewer', 'ggplot2', 'ggplot2movies', 'jsonlite',
  'knitr', 'shiny', 'binom', 'dplyr'

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
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'dplyr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'numDeriv', 'robustbase'

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

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:
  'geodist', 'hms', 'httr', 'jsonlite', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'digest', 'fields', 'Formula',
  'formula.tools', 'ggplot2', 'gtable', 'lubridate', 'memoise', 'plyr',
  'scales', 'sp', 'stringr', 'purrr', 'RCurl', 'isoband'

Packages suggested but not available for checking:
  'maps', 'maptools', 'covr', 'irlba', 'knitr', 'ncdf4', 'pkgdown',
  'reshape2', 'rmarkdown', 'testthat', 'viridis', 'udunits2',
  'gridExtra', 'vdiffr', 'proj4', 'kriging', 'raster', 'rgdal', 'here'

VignetteBuilder 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', 'matlab', 'leaflet', 'plyr', 'RCurl'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'prodlim', 'cmprsk', 'testthat', 'ucminf', 'knitr', 'bookdown',
  'rmarkdown', 'ggplot2', '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:
  'foreach', 'readr', 'stringr', 'tibble'

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

Packages suggested but not available for checking:
  'cobs', 'knitr', 'mvPot', 'mvtnorm', 'gmm', 'revdbayes', 'ismev'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mev-vignette.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.
show,mewTyp: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Packages required but not available: 'statmod', 'numDeriv', 'lamW'

Package suggested but not available for checking: 'rstpm2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'lubridate', 'GIGrvg', 'stochvol', 'RcppParallel',
  'dplyr', 'magrittr', 'tibble', 'zoo', 'RcppArmadillo', 'RcppProgress'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'ggridges', 'alfred', 'factorstochvol'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'logging', 'DBI', 'getPass', 'RPostgreSQL'

Packages suggested but not available for checking:
  'unittest', 'dplyr', 'dbplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clusterCrit', 'ECoL', 'e1071', 'infotheo', 'rrcov'

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', 'numDeriv', 'zoo', 'maxLik'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fda.usc', 'deldir', 'depth', 'depthTools', 'matrixStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tseries', 'pastecs', 'locfit', 'tseriesChaos', 'tsDyn', 'forecast'
Packages required but not available: 'dtw', '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:
  'funData', 'abind', 'foreach', 'irlba', 'plyr'

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

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 required but not available: 'ars', 'HI', 'coda'

Packages suggested but not available for checking:
  'sns', 'RcppArmadillo', 'inline', 'mvtnorm'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dataRetrieval', 'lmomco'
Packages required but not available: 'abind', 'energy', 'raster'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'reshape2', '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:
  'qgam', 'ggplot2', 'rgl', 'gamm4', 'matrixStats', 'viridis',
  'GGally', 'gridExtra', 'plyr', 'shiny', 'miniUI'

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: 'deSolve'

Packages suggested but not available for checking:
  'MGDrivE', '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: 'R6', 'Rcpp', '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: 'ggplot2'

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

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:
  'ggplot2', 'plyr', 'reshape2', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'mvnfast', 'plyr', '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:
  'matrixcalc', 'glmnet', 'stringr', 'Hmisc', 'qgraph', 'gtools'

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RJSONIO'
'library' or 'require' call to 'RJSONIO' 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'
.onAttach: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible global function definition for 'fromJSON'
call.MGRAST: no visible binding for global variable '.MGRAST'
call.MGRAST: no visible global function definition for 'download.file'
call.MGRAST: no visible global function definition for 'isValidJSON'
call.MGRAST: no visible global function definition for 'fromJSON'
doc.MGRAST: no visible binding for global variable '.MGRAST'
doc.MGRAST: no visible global function definition for 'str'
load.MGRAST: no visible binding for global variable '.MGRAST'
parse.MGRAST: no visible binding for global variable '.MGRAST'
this.package: no visible binding for global variable '.MGRAST'
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'combinat', 'statmod', 'rTensor'

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:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'qdap', 'microbenchmark'

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: 'Biobase', 'GSA', 'limma', 'ismev'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'sp', 'leaflet', 'spgwr', 'doParallel', 'foreach',
  'htmltools', 'nabor', '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.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
BCI: no visible global function definition for 'quantile'
Metro_Hastings: no visible global function definition for 'optim'
Metro_Hastings: no visible global function definition for 'runif'
Metro_Hastings: no visible global function definition for 'var'
plotMH: no visible global function definition for 'hist'
plotMH: no visible global function definition for 'frame'
plotMH: no visible global function definition for 'text'
Undefined global functions or variables:
  frame hist optim quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'plot3D', 'rootSolve', 'RcppArmadillo'

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

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 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: 'MCMCpack', 'mvtnorm', 'Rdpack'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'alluvial', 'RColorBrewer', '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', 'reshape2', 'gridExtra', 'RcppArmadillo', 'BH'

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', 'reshape2'

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/vignette1.Rnw'
(Is a VignetteBuilder field missing?)

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

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

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:
  'structSSI', 'MHTdiscrete', 'FixSeqMTP'
Package unavailable to check Rd xrefs: 'MHTdiscrete'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Formula', 'truncreg', 'maxLik', 'texreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'e1071', 'raster', 'rlang'

Packages suggested but not available for checking:
  'knitr', '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: '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.
Packages required but not available:
  'mice', 'mitools', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'blme', 'car', 'CDM', 'coda', 'grouped', 'imputeR',
  'inline', 'lme4', 'MBESS', 'MCMCglmm', 'mdmb', 'numDeriv', 'readxl',
  'sandwich', 'simputation', 'sirt', 'sjlabelled', 'synthpop', 'TAM'

Packages which this enhances but not available for checking:
  'Amelia', 'jomo', 'micemd', 'mitml', 'pan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lmtest', 'micEcon', 'systemfit', 'miscTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'minpack.lm', 'DEoptim', 'car', 'systemfit', 'micEcon', 'miscTools'

Packages suggested but not available for checking:
  'maxLik', 'xtable', 'AER'

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

Packages suggested but not available for checking: 'Ecdat', 'micEcon'

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

Packages suggested but not available for checking: 'Ecdat', 'systemfit'

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

Package suggested but not available for checking: 'micEcon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'magrittr', 'Rcpp', 'UpSetR', 'ggplot2',
  'tidyr', 'assertthat', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pacman', 'testthat', 'mice', 'broom', 'car'

VignetteBuilder 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', 'lme4', 'mvmeta', 'jomo', 'mvtnorm', 'digest', 'abind'

Package suggested but not available for checking: 'VIM'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ranger', 'data.table', 'FNN', 'ggplot2', 'crayon', 'corrplot',
  'ggpubr', 'DescTools', 'foreach'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'doParallel', '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', 'dplyr', 'generics', 'Rcpp', 'rlang', 'tidyr', 'cpp11'

Packages suggested but not available for checking:
  'broom.mixed', 'haven', 'knitr', 'lme4', 'metafor', 'mitml',
  'miceadds', 'pan', 'randomForest', 'rmarkdown', 'testthat', 'lmtest'

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'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doBy', 'combinat', 'flexclust', 'irr', 'matrixStats'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'biotools', 'MVN', 'deseasonalize', 'testthat', 'knitr', 'roxygen2',
  'devtools'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/paper.Rnw'
   'inst/doc/tolatex-examples.Rnw'
(Is a VignetteBuilder field missing?)
Packages unavailable to check Rd xrefs: 'MVN', 'biotools'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/paper.Rnw'
   'vignettes/tolatex-examples.Rnw'
(Is a VignetteBuilder field missing?)
Running examples in 'micompr-Ex.R' failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'nleqslv', 'distr'

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:
  'ggplot2', 'multcomp', 'RUnit'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'plyr', 'magrittr', 'broom', 'phyloseq', 'vegan', 'rlang',
  'ggplot2', 'ggpubr', 'DESeq2', 'dada2', 'SummarizedExperiment',
  'S4Vectors', 'Biostrings', 'rstatix', 'tidyr', 'DECIPHER',
  'phangorn', 'randomForest', 'edgeR', 'testthat'

Packages suggested but not available for checking:
  'markdown', '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:
  'microseq', 'microcontax', 'dplyr', 'stringr', 'rlang', 'Rcpp',
  'RcppParallel', 'tibble', '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: '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: 'microseq'

Package suggested but not available for checking: 'microcontax.data'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'ape', 'vegan', 'rlang', 'data.table', 'magrittr', 'dplyr',
  'tibble', 'scales', 'ggplot2', 'RColorBrewer'

Packages suggested but not available for checking:
  'reshape2', 'GUniFrac', 'ggpubr', 'randomForest', 'ggdendro',
  'ggrepel', 'agricolae', 'gridExtra', 'picante', 'pheatmap', 'igraph',
  'rgexf', 'tidytree', 'mice', 'ggtree', 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'dplyr', 'ggplot2', 'gtools', 'magrittr', 'scales', 'shiny',
  'shinyBS', 'tidyr', 'shinyWidgets', 'ggiraph'

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:
  'maptools', 'RColorBrewer', 'rgdal', 'sp', 'ggplot2'

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

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

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: 'ggplot2', 'reshape2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Hmisc', 'HH', 'flextable', 'officer', 'ggplot2', 'htmltools',
  'cowplot'

Packages suggested but not available for checking:
  'reshape2', 'latticeExtra', 'xtable', 'markdown', 'rmarkdown',
  'knitr', 'htmlTable'

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

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:
  'Rcpp', 'abind', 'deSolve', 'devtools', 'ggplot2', 'gridExtra',
  'gtools', 'knitr', 'matrixStats', 'matrixcalc', 'plyr', 'readr',
  'reshape2', 'shiny', 'stringr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bookdown', 'data.table', 'plotly', 'shinyjs', 'shinyBS',
  'rmarkdown', 'rhandsontable', 'shinycssloaders', '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:
  'tidyr', 'openxlsx', 'data.table', 'R.utils', 'stringr', 'magrittr',
  'dplyr', 'gtools', 'Biostrings', 'GenomicAlignments', 'Rsamtools',
  'GenomeInfoDb', 'BiocGenerics'

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10', '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:
  'tibble', 'stringr', 'dplyr', 'data.table', 'rlang', 'Rcpp'

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

Packages suggested but not available for checking:
  'testthat', 'usethis', 'httptest', 'plumber', 'jsonlite', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ascii', '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:
  'AzureAuth', 'AzureGraph', 'curl', 'httr', 'jsonlite', 'R6', 'vctrs',
  'mime'

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

VignetteBuilder 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', 'kernlab', 'LowRankQP', 'nleqslv', 'pracma'

Packages suggested but not available for checking:
  'xlsx', '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: 'chron', 'snowfall', 'rlecuyer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'gbm', 'genefilter', 'limma', 'preprocessCore', 'pROC',
  'SQN'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sandwich', 'optimx', 'quantreg', 'numDeriv', 'forecast', 'zoo',
  'Formula', 'texreg'

Packages suggested but not available for checking:
  'testthat', 'lubridate', 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mice'
'LazyData' is specified without a 'data' directory
Running examples in 'midastouch-Ex.R' failed
The error most likely occurred in:

> ### Name: mice.impute.midastouch
> ### Title: Predictive Mean Matching with distance aided selection of donors
> ### Aliases: mice.impute.midastouch midastouch
> ### Keywords: mice
> 
> ### ** Examples
> 
> ## from R:: mice, slightly adapted ##
> 
> # do default multiple imputation on a numeric matrix
> library(midastouch)
> library(mice)
Error in library(mice) : there is no package called 'mice'
Execution halted
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: 'BiasedUrn'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'tidygraph', 'ggplot2', 'ggraph', 'R6', 'magrittr',
  'rlang', 'dplyr', 'purrr', 'tibble', 'tidyr', 'network'

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

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

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

Packages suggested but not available for checking:
  'magrittr', '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: 'gWidgets2', 'mi', 'arm'

Package suggested but not available for checking: 'gWidgets2RGtk2'

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

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

Packages suggested but not available for checking:
  'igraph', 'ggplot2', 'gridExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'dplyr', 'e1071', 'glmnet', 'kernlab', 'MLmetrics',
  'randomForest', 'rlang', 'xgboost'

Packages suggested but not available for checking:
  'doFuture', 'foreach', 'future', 'future.apply', 'ggplot2', 'knitr',
  'purrr', 'rmarkdown', 'testthat', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
nat_hist: no visible global function definition for 'data'
nat_hist: no visible binding for global variable 'current.other'
t_mal: no visible global function definition for 'uniroot'
t_prog: no visible global function definition for 'rlnorm'
tdeath_lung: no visible global function definition for 'data'
tdeath_lung: no visible binding for global variable 'ci.lung'
tdeath_lung: no visible binding for global variable 'current.other'
tdeath_lung: no visible binding for global variable 'former.other'
tdeath_lung: no visible binding for global variable 'never.other'
tdeath_other: no visible global function definition for 'data'
tdeath_other: no visible binding for global variable 'ci.lung'
tdeath_other: no visible binding for global variable 'current.other'
tdeath_other: no visible binding for global variable 'former.other'
tdeath_other: no visible binding for global variable 'never.other'
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages required but not available: 'data.table', 'geepack'

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

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:
  'pipeR', 'numDeriv', 'glmnet', 'Rcpp', 'RcppParallel',
  'RcppArmadillo'

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

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:
  'glmnet', 'softImpute', 'FactoMineR', 'doParallel', 'foreach',
  'data.table', 'rARPACK'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mitools'
Malformed Description field: should contain one or more complete sentences.
MImix.default: no visible binding for global variable 'coef'
MImix.default: no visible binding for global variable 'vcov'
MImix.one: no visible global function definition for 'qnorm'
MImix.one: no visible global function definition for 'uniroot'
mixcdf.target: no visible global function definition for 'pnorm'
print.MImixresult: no visible global function definition for 'coef'
print.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'coef'
summary.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'qt'
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
Running examples in 'MImix-Ex.R' failed
The error most likely occurred in:

> ### Name: diaph.data
> ### Title: Diaphanography Partial Verification Bias Example
> ### Aliases: diaph.data
> 
> ### ** Examples
> 
> data(diaph.data)
> attach(diaph.data)
> ## Calculate sensitivity for each imputed table
> 
> sens.imps<-lapply(imputed.tables,function(x){ x[2,2]/(x[2,1]+x[2,2]) })
> sens.imps.vars<-lapply(imputed.tables,function(x){ x[2,2]*x[2,1]/(x[2,1]+x[2,2])^3 })
> 
> ### Calculate mixture summary
> 
> MImix(sens.imps,sens.imps.vars)
  2.5%ile    50%ile  97.5%ile 
0.1667023 0.2989993 0.5167686 
> 
> ### Compare to usual t-summary using MIcombine: requires(mitools)
> 
> library(mitools)
Error in library(mitools) : there is no package called 'mitools'
Execution halted
Packages required but not available:
  'caTools', 'dplyr', 'lubridate', 'magrittr', 'matlab', 'plyr',
  'readr', 'R.utils', 'signal', 'stringr', 'xts', 'dygraphs', 'shiny',
  'RColorBrewer', 'ggplot2'

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

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

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

VignetteBuilder 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', 'sp', 'maxnet', 'dismo', 'ecospat', 'geosphere',
  'latticeExtra'

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', 'data.table', 'digest', 'jsonlite', 'memoise', 'xts'

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

VignetteBuilder 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', 'knitr', 'jsonlite', 'data.tree'

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: 'Iso', 'ggplot2', 'gridExtra'

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.
miney : plot.initial.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'text'
miney: no visible global function definition for 'locator'
miney: no visible global function definition for 'rect'
miney: no visible global function definition for 'title'
Undefined global functions or variables:
  locator rect text title
Consider adding
  importFrom("graphics", "locator", "rect", "text", "title")
to your NAMESPACE file.
Packages required but not available: 'httr', 'igraph', 'assertthat'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'testthat', 'covr', 'withr',
  'mockery', 'testthis', '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:
  'htmltools', 'knitr', 'rmarkdown', 'xfun'

Packages suggested but not available for checking:
  'callr', 'dplyr', 'purrr', 'testthat', 'tidyr', 'tibble'

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: 'stats'
  All declared Imports should be used.
'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
rminimax: 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:
  'meta', 'shiny', 'shinyjs', 'shinyWidgets', 'colourpicker',
  'rhandsontable', 'metafor', 'markdown', 'WriteXLS', 'readxl',
  '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: 'V8'

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

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: 'glasso', 'trust', 'testthat'

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'sybil', 'glpkAPI'

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
minxent.multiple: no visible global function definition for 'cov.wt'
minxent.single: no visible global function definition for 'optimize'
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
Packages required but not available: 'cmm', 'Rsolnp', 'numDeriv'

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

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

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

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: 'RandomFieldsUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.FCLoess: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'median'
.Import.Luminex: no visible global function definition for 'read.csv'
.Intra.Me: no visible global function definition for 'sd'
.Intra.Me: no visible global function definition for 'quantile'
.Intra.Me: no visible global function definition for 'qchisq'
.Intra.Median: no visible global function definition for 'median'
.boxplot.rtprofile: no visible global function definition for 'boxplot'
.denplot: no visible global function definition for 'density'
.denplot: no visible global function definition for 'abline'
.normalize.Luminex: no visible global function definition for 'sd'
.normalize.qrtpcr: no visible global function definition for 'density'
.validate.default: no visible global function definition for 't.test'
Undefined global functions or variables:
  abline boxplot density loess median qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'npmv', 'dendextend', 'plyr', 'reshape2', 'ArgumentCheck'

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

Packages suggested but not available for checking:
  'betareg', 'knitr', 'sn', 'truncnorm'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'Formula', 'mvtnorm',
  'dirichletprocess', 'truncnorm', 'pracma', 'cubature', 'logspline',
  'HDInterval', '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:
  'CompQuadForm', 'quantreg', 'GUniFrac', 'PearsonDS', 'lme4',
  'permute', 'mixtools'

Packages suggested but not available for checking:
  'knitr', 'propr', 'dirmult', 'vegan', 'rmarkdown', 'tidyverse',
  'kableExtra'

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: 'ggplot2', 'pROC'

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', 'CORElearn', 'RSpectra'

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

Packages suggested but not available for checking:
  'shinythemes', 'SimDesign', '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:
  'corpcor', 'globaltest', 'GlobalAncova', 'limma', 'RepeatedHighDim'

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

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

Packages suggested but not available for checking:
  'latticeExtra', 'directlabels', 'shiny', 'knitr', 'markdown',
  'Rsolnp', 'nloptr', 'sirt', 'plink', 'mirtCAT'

VignetteBuilder 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', 'mirtjml'

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

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

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: 'rgl', 'tkrplot'
Packages unavailable to check Rd xrefs: 'rgl', 'scatterplot3d'
Running examples in 'misc3d-Ex.R' failed
The error most likely occurred in:

> ### Name: contour3d
> ### Title: Draw an Isosurface, a Three Dimension Contour Plot
> ### Aliases: contour3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: Draw a ball
>   f <- function(x, y, z)x^2+y^2+z^2
>   x <- seq(-2,2,len=20)
>   contour3d(f,4,x,x,x)
Error in loadRGL() : rgl is mot available
Calls: contour3d -> drawScene.rgl -> loadRGL
Execution halted
Packages required but not available: 'R2jags', 'MCMCpack', 'mvtnorm'

Packages suggested but not available for checking: 'mixAK', 'BRugs'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ucminf', 'numDeriv', 'bigmemory', 'foreach', 'mlogit'

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
Packages required but not available:
  'data.table', 'devtools', 'ggplot2', 'gridExtra', 'Rcpp', 'xtable'

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.
Package required but not available: 'digest'

Package suggested but not available for checking: 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'mice', '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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'e1071', 'penalized'

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

Package suggested but not available for checking: 'ade4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'numDeriv', 'VGAM', '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:
  'Amelia', 'data.table', 'dplyr', 'ggdendro', 'ggplot2', 'Hmisc',
  'ltm', 'magrittr', 'mi', 'mice', 'missForest', 'missMDA',
  'pcaMethods', 'plyr', 'rlang', 'tidyr', 'VIM'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', '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:
  'rms', 'relsurv', 'cmprsk', 'Rcpp', 'mitools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mcmcplots', 'ggpubr', 'ggmcmc', 'ggthemes', 'BCEA', 'ggplot2',
  'gridExtra', 'bayesplot', 'R2jags', 'loo', 'coda', 'mcmcr'

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:
  'FactoMineR', 'ggplot2', 'mice', 'mvtnorm', 'doParallel', 'foreach'

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'lpSolve', 'mvtnorm', 'norm', 'rmarkdown',
  'testthat', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'norm'
'LazyData' is specified without a 'data' directory
Running examples in 'missMethods-Ex.R' failed
The error most likely occurred in:

> ### Name: impute_EM
> ### Title: EM imputation
> ### Aliases: impute_EM
> 
> ### ** Examples
> 
> ds_orig <- mvtnorm::rmvnorm(100, rep(0, 7))
Error in loadNamespace(x) : there is no package called 'mvtnorm'
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: 'ranger', 'FNN'

Packages suggested but not available for checking:
  'dplyr', 'mice', 'rmarkdown', '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', 'ape', 'igraph', 'nloptr', 'ggplot2', 'corrplot', 'R6',
  'rlang', 'sbm', 'magrittr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'aricode', 'blockmodels', '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 suggested but not available for checking:
  'e1071', 'mvtnorm', 'AcceptanceSampling', 'car', 'Dodge', 'tseries',
  'qcc', 'DoE.base', 'FrF2', 'rsm', 'LearnBayes', 'ggplot2',
  'DiceEval', 'DiceKriging', 'DiceDesign', 'DiceView', 'lhs',
  'fdapace', 'randomForest', 'xgboost'
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'qcc', 'AcceptanceSampling', 'FrF2'
Running examples in 'mistat-Ex.R' failed
The error most likely occurred in:

> ### Name: CONTACTLEN
> ### Title: Length of the Electrical Contacts
> ### Aliases: CONTACTLEN
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(CONTACTLEN)
> 
> library(qcc)
Error in library(qcc) : there is no package called 'qcc'
Execution halted
Packages required but not available:
  'e1071', 'mvtnorm', 'ggplot2', 'doParallel', 'foreach', 'iterators',
  'DiceKriging', 'emoa', 'quadprog', 'Rcpp'

Packages suggested but not available for checking:
  'microbenchmark', 'deSolve', 'scatterplot3d', 'KrigInv', 'rgenoud',
  'kernlab', 'knitr', 'rmarkdown', 'markdown'

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: 'CompQuadForm'

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

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

VignetteBuilder 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', 'lavaan', 'lme4', 'readxl'

Packages suggested but not available for checking:
  'mnormt', 'plyr', '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: 'mvtnorm'

Package suggested but not available for checking: 'AdMit'

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

Packages suggested but not available for checking:
  'mice', 'miceadds', 'Amelia', 'lme4', 'lavaan', 'geepack', '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: 'DBI'

Package suggested but not available for checking: 'RODBC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'plyr', 'tidyr', 'xml2', 'rvest', 'jsonlite', 'RJSONIO',
  'stringr', 'httr', 'yaml', 'rlang', 'igraph'

Packages suggested but not available for checking:
  'visNetwork', 'knitr', 'rmarkdown', 'shiny', 'curl', '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: 'stabledist'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'animation', '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:
  'coda', 'condMVNorm', 'ggplot2', 'glm2', 'Hmisc', 'invgamma',
  'matrixNormal', 'MCMCpack', 'mvtnorm', 'purrr', 'rlist', 'Rsolnp',
  'tidyr', 'tmvmixnorm', 'tmvtnorm', 'truncnorm'

Packages suggested but not available for checking:
  'formatR', 'GGally', 'knitr', 'mice', 'norm', 'pander', 'rmarkdown',
  'scales', 'sessioninfo', 'spelling', 'testthat', 'wqs'

VignetteBuilder 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', 'lme4', 'fastGHQuad', 'mnormt', 'coda'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BB', 'combinat', 'timeDate', 'fGarch', 'Rdpack', 'gbutils',
  'MCMCpack', 'e1071', 'permute', 'mvtnorm'

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

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:
  'minpack.lm', 'nloptr', 'zoo', 'tmvtnorm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', '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:
  'expm', 'matrixcalc', 'Rsolnp', 'kdensity'

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: 'flexsurv', 'survey', 'gam', 'timereg'

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

Packages suggested but not available for checking:
  'testthat', 'tibble', 'purrr', 'dplyr', 'rmutil', 'pheatmap',
  'mcclust', 'ggplot2', 'tidyr'

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'ordinalClust', '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', 'gtools', 'RcppArmadillo', 'BH'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'beepr', 'brglm', 'lme4', 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sde', 'moments', 'plot3D'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'fftw', 'MixSim', 'EMCluster'

Packages which this enhances but not available for checking:
  'pbdMPI', 'AnalyzeFMRI', 'oro.nifti'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Bessel', 'mvtnorm', 'ghyp', 'numDeriv', 'mixture', 'e1071'

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', '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:
  'mixOmics', 'ggplot2', 'reticulate', 'vegan', 'phyloseq', 'corrplot',
  'psych', 'quadprog', 'LDRTools'

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

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

Package suggested but not available for checking: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maxLik', 'numDeriv', 'randtoolbox', 'Rcpp', 'readr', 'sandwich',
  'stringr'

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

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: 'lme4'

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

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

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:
  'metafor', 'meta', 'rmeta', 'dosresmeta', 'dlnm'
Packages unavailable to check Rd xrefs: 'metafor', 'mvmeta', 'dosresmeta'
Running examples in 'mixmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: alcohol
> ### Title: Alcohol Intake and Colorectal Cancer
> ### Aliases: alcohol
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ### REPRODUCE THE RESULTS IN CRIPPA ET AL (2016) AND ORSINI ET AL (2012)
> 
> # LOAD THE PACKAGE dosresmeta AND splines
> library(dosresmeta) ; library(splines)
Error in library(dosresmeta) : there is no package called 'dosresmeta'
Execution halted
Packages required but not available:
  'ggplot2', 'patchwork', 'desirability', '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:
  'pbapply', 'Formula', 'Rfast', 'dplyr', 'gamlss.dist', 'generics',
  'ggplot2', 'gridExtra', 'lmtest', 'magrittr', 'statmod', 'tibble',
  'rlang', 'ggrepel', 'gamlss'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'devtools', 'bbreg', 'testthat', 'covr',
  'tidyr', 'ggfortify', 'broom'

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:
  'knitr', 'rmarkdown', 'mixRasch', 'testthat'
Packages required but not available:
  'doParallel', 'randomForest', 'lme4', 'foreach'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'R2jags', 'RColorBrewer', 'reshape', 'reshape2',
  'MCMCpack', 'ggmcmc', 'coda', 'loo', 'bayesplot', 'splancs'

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 which this enhances but not available for checking: 'mclust'
'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: '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: 'irlba', 'Rcpp', 'RcppArmadillo'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
fit.mixtNB: no visible global function definition for 'dnbinom'
fit.mixtNB: no visible global function definition for 'nlminb'
wald.test: no visible global function definition for 'pnorm'
wald.test: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
Packages required but not available: 'kernlab', 'segmented'

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

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:
  'Rcpp', 'RcppArmadillo', 'BH', 'RcppGSL'

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

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
Packages required but not available:
  'assertthat', 'deSolve', 'dplyr', 'ggplot2', 'plotly', 'plyr',
  'progress', 'Rcpp', 'reshape2', 'lifecycle'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'roxygen2', 'knitr', 'shinyBS', 'rmarkdown',
  'pkgdown', 'covr', 'spelling'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'rms'
Packages required but not available: 'Rcpp', 'raster', 'sp'

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', '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: 'MKdescr', 'arrangements', 'ggplot2'

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

VignetteBuilder 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', 'R6', 'inline', 'numDeriv', 'lmtest', 'pkgbuild', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rbenchmark', 'tikzDevice', 'testthat', 'rmarkdown', 'covr',
  'vdiffr', 'benchmarkme', 'tibble'

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.
Malformed Description field: should contain one or more complete sentences.
mkle: no visible global function definition for 'sd'
mkle: no visible global function definition for 'density'
mkle: no visible global function definition for 'optimize'
mkle.ci: no visible global function definition for 'sd'
mkle.ci: no visible binding for global variable 'var'
mkle.ci: no visible global function definition for 'quantile'
mkle.ci: no visible global function definition for 'qnorm'
opt.bw: no visible global function definition for 'sd'
opt.bw : mse: no visible global function definition for 'var'
opt.bw: no visible global function definition for 'optimize'
opt.bw: no visible global function definition for 'var'
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
Packages required but not available:
  'RColorBrewer', 'robustbase', 'ggplot2', 'scales', 'limma'

Packages suggested but not available for checking:
  'gplots', 'Amelia', 'knitr', 'rmarkdown', 'exactRankTests',
  'foreach', '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: 'assertthat', 'data.table', 'lpSolve'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'Rglpk', 'ROI', 'ROI.plugin.glpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RColorBrewer', 'robustbase', '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:
  'matrixTests', 'ggplot2', 'MKdescr', 'MKinfer', 'qqplotr', 'coin'

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.
mkssd: no visible global function definition for 'txtProgressBar'
mkssd: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages required but not available:
  'keras', 'reticulate', 'tensorflow', 'tfprobability'

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'limSolve', 'MultiLCIRT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'klaR', 'dplyr', 'caret', 'DiscriMiner',
  'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'klaR', 'dplyr', 'caret', 'DiscriMiner',
  'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mldr'
Packages required but not available: 'shiny', 'XML', 'circlize'

Packages suggested but not available for checking:
  'pROC', 'knitr', 'mldr.datasets', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'fs', 'jsonlite', 'purrr', 'rJava', 'sparklyr', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'randomForest', 'ipred'

Packages suggested but not available for checking:
  'mlbench', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plotCDF1: no visible global function definition for 'lines'
plotCDF2: no visible global function definition for 'gray'
plotCDF2: no visible global function definition for 'image'
plotCDF2: no visible global function definition for 'box'
plotCDF2: no visible global function definition for 'par'
plotCDF2: no visible global function definition for 'rect'
plotCDF2: no visible global function definition for 'text'
plotCM: no visible global function definition for 'image'
plotCM: no visible global function definition for 'axis'
plotCM: no visible global function definition for 'box'
plotDens1: no visible global function definition for 'lines'
plotDens2: no visible global function definition for 'gray'
plotDens2: no visible global function definition for 'rect'
plotDens2: no visible global function definition for 'axis'
plotDens2: no visible global function definition for 'text'
plotHM: no visible global function definition for 'terrain.colors'
plotHM: no visible global function definition for 'image'
plotHM: no visible global function definition for 'box'
plotHM: no visible global function definition for 'abline'
plotHM: no visible global function definition for 'text'
plotHM: no visible global function definition for 'par'
plotHM: no visible global function definition for 'rect'
plotRects: no visible global function definition for 'rainbow'
plotRects: no visible global function definition for 'abline'
plotRects: no visible global function definition for 'rect'
Undefined global functions or variables:
  abline axis box gray image lines par rainbow rect terrain.colors text
Consider adding
  importFrom("grDevices", "gray", "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "rect", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'snowfall'
Packages required but not available:
  'ergm', 'network', 'stringr', 'GGally', 'ggplot2', 'cowplot',
  'reshape2', 'plyr', 'lpSolve', 'sna'

Packages suggested but not available for checking:
  'RColorBrewer', '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: 'fitdistrplus'
Running examples in 'mle.tools-Ex.R' failed
The error most likely occurred in:

> ### Name: coxsnell.bc
> ### Title: Bias-Corrected Maximum Likelihood Estimate(s)
> ### Aliases: coxsnell.bc
> 
> ### ** Examples
> 
> {library(mle.tools); library(fitdistrplus); set.seed(1)};
Error in library(fitdistrplus) : 
  there is no package called 'fitdistrplus'
Execution halted
Packages required but not available: 'urca', 'stabledist', 'fGarch'

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:
  'base64enc', 'forge', 'fs', 'git2r', 'glue', 'httpuv', 'httr', 'ini',
  'jsonlite', 'openssl', 'processx', 'purrr', 'reticulate', 'rlang',
  'swagger', 'tibble', 'withr', 'xml2', 'yaml', 'zeallot'

Packages suggested but not available for checking:
  'carrier', 'covr', 'h2o', 'keras', 'lintr', 'mleap', 'sparklyr',
  'stringi', 'testthat', 'xgboost'

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

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

Package suggested but not available for checking: 'snowfall'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CheckStability: no visible global function definition for 'cor'
CheckStability: no visible global function definition for 'var'
PriorNormPCA: no visible global function definition for 'barplot'
SortModes: no visible global function definition for 'rnorm'
mlicaMAIN: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'lme4'

Packages suggested but not available for checking:
  'raster', 'sp', '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', 'car', 'abind', 'coxme', 'gplots'

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', 'Rcpp'

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

Package suggested but not available for checking: 'e1071'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'minfi', 'microbenchmark', 'GEOquery', 'knitr', 'rmarkdown',
  'IlluminaHumanMethylation450kmanifest'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'multcompView', 'multcomp', 'coxme', 'sommer'

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', 'RcppDist'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'XLConnect', 'rJava', 'Rdpack', '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.
Package required but not available: 'lme4'

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

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

Package suggested but not available for checking: 'mlogit'

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

Packages suggested but not available for checking:
  'knitr', 'car', 'AER', 'ggplot2', 'texreg', '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', 'BH', 'RcppEnsmallen'

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: 'Biostrings'
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
Skipping vignette re-building
Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'
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Package suggested but not available for checking: 'CORElearn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'ggplot2', 'mlr3misc', 'R6'

Packages suggested but not available for checking:
  'mlr3', 'mlr3learners', 'PMCMR', 'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'clue', 'clusterCrit', 'data.table',
  'mlr3', 'mlr3misc', 'paradox', 'R6'

Packages suggested but not available for checking:
  'dbscan', 'e1071', 'ClusterR', 'kernlab', 'apcluster', 'LPCM',
  'mlbench', 'RWeka', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mlr3'
Packages required but not available:
  'mlr3', 'R6', 'backports', 'checkmate', 'data.table', 'digest',
  'mlr3misc'

Packages suggested but not available for checking:
  'DBI', 'RSQLite', 'dbplyr', 'dplyr', 'duckdb', 'future',
  'future.apply', 'future.callr', 'lgr', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'mlr3', 'mlr3misc',
  'paradox', 'R6'

Packages suggested but not available for checking:
  'care', 'caret', 'FSelectorRcpp', 'lgr', 'mlr3learners',
  'mlr3measures', 'praznik', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bbotk', 'checkmate', 'data.table', 'lgr', 'mlr3', 'mlr3misc',
  'mlr3pipelines', 'paradox', 'R6'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3tuning', 'bbotk', 'checkmate', 'data.table', 'lgr', 'mlr3',
  'mlr3misc', 'paradox', 'R6'

Packages suggested but not available for checking:
  'emoa', 'mlr3learners', 'mlr3pipelines', 'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'data.table', 'mlr3misc', 'paradox', 'R6'

Packages suggested but not available for checking:
  'checkmate', 'DiceKriging', 'distr6', 'e1071', 'glmnet', 'kknn',
  'knitr', 'lgr', 'mlr3proba', 'pracma', 'ranger', 'rgenoud',
  'rmarkdown', 'testthat', 'xgboost'

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'curl', 'data.table', 'jsonlite', 'lgr',
  'mlr3', 'mlr3misc', 'R6', 'stringi'

Packages suggested but not available for checking:
  'RWeka', 'farff', 'qs', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'digest', 'lgr', 'mlr3',
  'mlr3misc', 'paradox', 'R6', 'withr'

Packages suggested but not available for checking:
  'ggplot2', 'glmnet', 'igraph', 'knitr', 'lme4', 'mlbench', 'bbotk',
  'mlr3filters', 'mlr3learners', 'mlr3measures', 'nloptr', 'quanteda',
  'rmarkdown', 'stopwords', 'testthat', 'visNetwork', 'bestNormalize',
  'fastICA', 'kernlab', 'smotefamily', 'evaluate', 'NMF', 'kknn',
  'GenSA', 'vtreat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'distr6', 'mlr3', 'mlr3misc', 'paradox',
  'R6', 'Rcpp'

Packages suggested but not available for checking:
  'bujar', 'cubature', 'ggplot2', 'knitr', 'lgr', 'mlr3extralearners',
  'mlr3pipelines', 'pracma', 'set6', 'simsurv', 'survAUC', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'backports', 'checkmate', 'data.table', 'digest',
  'future.apply', 'lgr', 'mlbench', 'mlr3measures', 'mlr3misc',
  'parallelly', 'palmerpenguins', 'paradox', 'uuid'

Packages suggested but not available for checking:
  'callr', 'distr6', 'evaluate', 'future', 'future.callr', 'mlr3data',
  'progressr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'mlr3measures', 'mlr3learners', 'shiny', 'shinythemes',
  'shinydashboard', 'shinyjs', 'shinyWidgets', 'shinyalert',
  'data.table', 'DT', 'readxl', 'stringr', 'plyr', 'purrr', 'ranger',
  'e1071'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'ggplot2', 'mlr3', 'mlr3misc', 'paradox',
  'R6'

Packages suggested but not available for checking:
  'bbotk', 'blockCV', 'CAST', 'ggsci', 'ggtext', 'knitr', 'lgr',
  'mlr3filters', 'mlr3pipelines', 'mlr3tuning', 'patchwork', 'plotly',
  'raster', 'rmarkdown', 'sf', 'skmeans', 'testthat', 'vdiffr', '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:
  'mlr3', 'paradox', 'bbotk', 'checkmate', 'data.table', 'lgr',
  'mlr3misc', 'R6'

Packages suggested but not available for checking:
  'adagio', 'GenSA', 'mlr3pipelines', 'nloptr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bbotk', 'data.table', 'mlr3', 'mlr3cluster', 'mlr3data',
  'mlr3filters', 'mlr3fselect', 'mlr3learners', 'mlr3misc',
  'mlr3pipelines', 'mlr3proba', 'mlr3tuning', 'mlr3viz', 'paradox'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'ggplot2', 'mlr3misc'

Packages suggested but not available for checking:
  'distr6', 'factoextra', 'GGally', 'ggfortify', 'ggparty', 'glmnet',
  'lgr', 'mlr3', 'mlr3cluster', 'mlr3filters', 'mlr3learners',
  'mlr3proba', 'mlr3tuning', 'paradox', 'partykit', 'patchwork',
  'precrec', 'ranger', 'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ParamHelpers', 'mlr', 'BBmisc', 'stringi', 'checkmate', 'backports'

Packages suggested but not available for checking:
  'care', 'party', 'mlbench', 'knitr', 'rmarkdown', 'testthat',
  'mRMRe', 'praznik', 'randomForestSRC', 'randomForest', 'ranger',
  'Rfast', 'FSelector', 'FSelectorRcpp', 'e1071', 'DiscriMiner',
  'digest', 'lintr', 'Hmisc', 'fastICA', 'rex'

VignetteBuilder 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', 'checkmate', 'data.table', 'mlr3misc', 'paradox', 'R6',
  'lhs', 'callr', 'bbotk', 'mlr3tuning'

Packages suggested but not available for checking:
  'mlr', 'ParamHelpers', 'testthat', 'rgenoud', 'DiceKriging', 'emoa',
  'cmaesr', 'randomForest', 'smoof', 'lgr', 'mlr3', 'mlr3learners',
  'mlr3pipelines', 'mlrMBO', 'ranger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'ParamHelpers', 'smoof', 'backports', 'BBmisc', 'checkmate',
  'data.table', 'lhs', 'parallelMap'

Packages suggested but not available for checking:
  'akima', 'cmaesr', 'ggplot2', 'DiceKriging', 'earth', 'emoa',
  'GGally', 'gridExtra', 'kernlab', 'kknn', 'knitr', 'mco', 'party',
  'randomForest', 'reshape2', 'rmarkdown', 'rgenoud', '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:
  'ParamHelpers', 'backports', 'BBmisc', 'checkmate', 'data.table',
  'ggplot2', 'parallelMap', 'stringi', 'XML'

Packages suggested but not available for checking:
  'ada', 'adabag', 'bartMachine', 'batchtools', 'bit64', 'brnn', 'bst',
  'C50', 'care', 'caret', 'clue', 'ClusterR', 'clusterSim', 'cmaes',
  'cowplot', 'crs', 'Cubist', 'deepnet', 'DiceKriging', 'DiscriMiner',
  'e1071', 'earth', 'elasticnet', 'emoa', 'evtree', 'extraTrees',
  'fda.usc', 'FDboost', 'FNN', 'forecast', 'fpc', 'frbs', 'FSelector',
  'FSelectorRcpp', 'gbm', 'GenSA', 'ggpubr', 'glmnet', 'GPfit', 'h2o',
  'Hmisc', 'irace', 'kernlab', 'kknn', 'klaR', 'knitr', 'laGP',
  'LiblineaR', 'lintr', 'mboost', 'mco', 'mda', 'memoise', 'mlbench',
  'mldr', 'mlrMBO', 'mmpf', 'modeltools', 'mRMRe', 'neuralnet',
  'nodeHarvest', 'numDeriv', 'pamr', 'pander', 'party', 'pec',
  'penalized', 'pls', 'PMCMRplus', 'praznik', 'randomForest',
  'randomForestSRC', 'ranger', 'rappdirs', 'refund', 'rex', 'rFerns',
  'rgenoud', 'rknn', 'rmarkdown', 'Rmpi', 'ROCR', 'rotationForest',
  'RRF', 'rrlda', 'rsm', 'RSNNS', 'rucrdtw', 'RWeka', 'sda', 'sf',
  'smoof', 'snow', 'sparseLDA', 'stepPlr', 'survAUC', 'svglite',
  'SwarmSVM', 'testthat', 'tgp', 'TH.data', 'tidyr', 'tsfeatures',
  'vdiffr', 'wavelets', '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:
  'shiny', 'shinyAce', 'dplyr', 'psych', 'QuantPsyc', 'forecast',
  'corrgram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyAce', 'dplyr', 'psych', 'QuantPsyc', 'forecast',
  'corrgram'

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.
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:
  'mlt', 'numDeriv', 'eha', 'multcomp', 'flexsurv', 'truncreg', 'np'

Packages suggested but not available for checking:
  'variables', 'basefun', 'TH.data', 'knitr', 'prodlim', 'gridExtra',
  'HSAUR3', 'sandwich', 'latticeExtra', 'colorspace', 'coxinterval',
  'ICsurv', 'polspline', 'logspline', 'bshazard', 'gss', 'MIICD',
  'TransModel', 'dynsurv', 'timereg', 'survivalMPL', 'gamlss', 'muhaz',
  'ICE', 'ordinal', 'VGAM', 'AER', 'coin', 'gamlss.data', 'mlbench',
  'tram', 'rms'

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.
'LazyData' is specified without a 'data' directory
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:
  'basefun', 'variables', 'BB', 'alabama', 'coneproj', 'sandwich',
  'numDeriv', 'nloptr'

Packages suggested but not available for checking: 'TH.data', 'multcomp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'arm', 'qgraph', 'dplyr', 'clusterGeneration', 'mvtnorm',
  'corpcor', 'plyr', 'abind', 'MplusAutomation', 'graphicalVAR'

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

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

Packages suggested but not available for checking:
  'XML', 'Rcpp', 'reshape2', 'gridExtra', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gplots', 'ggplot2', 'reshape2', 'TMB', '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: 'Biobase'

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/MM2Sdata.Rnw'
(Is a VignetteBuilder field missing?)

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

Packages suggested but not available for checking: 'knitr', 'MM2Sdata'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/MM2S.Rnw'
   'inst/doc/MM2S_FromRawData.Rnw'
(Is a VignetteBuilder field missing?)

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: 'glmnet', 'mma', 'car', 'gplots'

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:
  'mosaic', 'mosaicCalc', 'manipulate'
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'loder', 'tinytest', 'covr'

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

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:
  'htmltools', 'Cairo', 'xts', 'lubridate', 'zoo', 'caTools',
  'ggplot2', 'data.table', 'DT', 'dplyr', 'leaflet', 'stringr',
  'shiny', 'XML', 'shinyjs', 'plotly'

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

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

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: 'Rdpack', 'foreach', 'doParallel'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'covr', 'e1071', 'caret', 'knitr',
  'rmarkdown', 'ggplot2', 'ggpubr', 'cowplot', 'philentropy', 'Rtsne'

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:
  'VineCopula', 'cubature', 'pcaPP', 'randtoolbox'

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: 'e1071', 'plyr', 'bigmemory'

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: 'Biobase', 'lawstat'

Package suggested but not available for checking: 'ALL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jointDiag', 'lme4', 'matrixcalc', 'psych', 'stringr'

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

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: 'gee'

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

Packages suggested but not available for checking: 'geepack', '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: 'adegenet', 'pegas'

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'

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

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:
  'testthat', 'rmarkdown', 'knitr', 'randomForest', 'ggplot2',
  'reshape2'

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'

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:
  'Oarray', 'partitions', 'magic', 'abind', 'emulator'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'reshape', 'reshape2', 'ggplot2', 'rlang', 'RcppArmadillo'

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 '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: 'flexsurv', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'dplyr', 'tibble', 'stringi', 'Rcpp', 'janitor',
  'purrr'

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: '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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'CDM', 'Rcpp', 'RcppArmadillo'

Packages which this enhances but not available for checking:
  'aMNLFA', 'GPCMlasso', 'sirt'

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

Package suggested but not available for checking: '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', 'testthat', 'magrittr', 'ggplot2', 'scales'

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: 'shiny', 'rmarkdown', 'e1071', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ICSNP', 'SpatialNP', 'ellipse', 'ICS'

Packages suggested but not available for checking:
  'Flury', 'gamlss', 'mvtnorm'

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

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'tmvnsim'

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: 'dplyr', 'tidyr', 'ggplot2', 'tibble'

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

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:
  'party', 'sandwich', 'strucchange', 'zoo', 'modeltools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'knitr', 'kableExtra', 'ggplot2', 'XML', 'plyr', 'yaml',
  'mailR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'covr', '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:
  'texmex', 'copBasic', 'ks', 'SpatialExtremes', 'zoo', 'copula',
  'ggplot2', 'viridis'

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 suggested but not available for checking:
  'EMMREML', 'BGLR', 'doMPI', 'doRNG', 'foreach', 'sommer', 'vcfR',
  'jsonlite', 'rrBLUP', 'biomaRt', 'doParallel'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages required but not available: 'gbm', 'Rborist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotrix', 'scales', 'dplyr', 'purrr', 'tidyr', 'pbapply', 'ggplot2',
  'egg', 'tibble', 'vctrs', 'rlang', 'geosphere'

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', 'vegan', 'sads'

Packages suggested but not available for checking:
  'rmarkdown', 'spatstat.geom', 'spatstat.core', 'spatstat',
  '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: 'cclust', 'clue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'amap', 'mco', 'nsga2R', 'reshape2', 'miscTools', 'matrixStats',
  'fields', 'Rmisc', 'plyr', 'foreach', 'doParallel', 'doSNOW', 'doMPI'

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: 'testthat'

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

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: 'lazyeval'

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:
  'testthat', 'pkgload', 'curl', 'jsonlite', 'withr'
Packages unavailable to check Rd xrefs: 'testthat', 'withr'
Running examples in 'mockthat-Ex.R' failed
The error most likely occurred in:

> ### Name: mock
> ### Title: Mocking helper functions
> ### Aliases: mock mock_call mock_args mock_arg mock_n_called
> 
> ### ** Examples
> 
> url <- "https://eu.httpbin.org/get?foo=123"
> 
> mk <- mock("mocked request")
> dl <- function(x) curl::curl(x)
> 
> with_mock(`curl::curl` = mk, dl(url))
Error in loadNamespace(name) : there is no package called 'curl'
Calls: with_mock ... 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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mvtnorm', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'RColorBrewer', 'collapsibleTree', 'dplyr', 'dygraphs',
  'highcharter', 'jsonlite', 'lazyeval', 'leaflet', 'networkD3',
  'plotly', 'rgdal', 'shiny', 'shinyBS', 'shinydashboard',
  'shinydashboardPlus', 'sp', 'sparkline', 'sunburstR', 'treemap',
  'htmlwidgets', 'magrittr'

Package suggested but not available for checking: 'modgetxl'

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

Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'tidyr', '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:
  'fBasics', 'stable', 'stabledist', 'statip'

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

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

Packages suggested but not available for checking:
  'mvtnorm', 'TH.data', 'psychotools', 'strucchange', 'plyr', 'knitr',
  'ggbeeswarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayestestR', 'emmeans', 'insight', 'parameters'

Packages suggested but not available for checking:
  'brms', 'coda', 'dplyr', 'effectsize', 'gamm4', 'gganimate',
  'ggplot2', 'glmmTMB', 'knitr', 'lme4', 'logspline', 'merTools',
  'rmarkdown', 'rstanarm', 'see', 'testthat', 'spelling'

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

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
Package suggested but not available for checking: 'covr'
Note: found 12 marked UTF-8 strings
Packages required but not available:
  'dplyr', 'rlang', 'purrr', 'tibble', 'progress', 'ggplot2',
  'tidypredict'

Packages suggested but not available for checking:
  'dbplyr', 'testthat', 'knitr', 'rmarkdown', 'nycflights13',
  'RSQLite', 'DBI', '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:
  'DALEX', 'auditor', 'ggplot2', 'whisker', 'DT', 'kableExtra',
  'psych', 'archivist', 'svglite', 'devtools', 'breakDown', 'drifter'

Packages suggested but not available for checking:
  'ranger', 'testthat', 'useful'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ClassDiscovery', 'ClassComparison', 'oompaBase', 'TailRank',
  'e1071', 'randomForest', 'neuralnet'

Package suggested but not available for checking: 'Biobase'

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

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

Packages suggested but not available for checking:
  'party', 'glmnet', 'rms', 'randomForest', 'randomForestSRC'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quantreg', 'coxrobust', '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:
  'randomForest', 'raster', 'rgdal', 'corrplot', 'fields',
  'HandTill2001', 'PresenceAbsence'

Packages suggested but not available for checking:
  'party', 'quantregForest'

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

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', 'gridExtra', 'magrittr', 'dplyr', 'RColorBrewer',
  'ggfittext', 'scales', 'rlang'

Packages suggested but not available for checking:
  'mlr', 'caret', 'randomForest', 'e1071', 'h2o', 'keras', 'knitr',
  'rmarkdown', 'testthat', 'xgboost', 'stringr', 'kableExtra',
  'ranger', '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:
  'broom', 'magrittr', 'purrr', 'rlang', 'tibble', 'tidyr',
  'tidyselect', 'vctrs'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DALEX', 'ingredients', 'iBreakDown', 'r2d3', 'jsonlite', 'progress',
  'digest'

Packages suggested but not available for checking:
  'parallelMap', 'ranger', 'xgboost', 'knitr', 'rmarkdown', '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:
  'broom', 'checkmate', 'generics', 'glue', 'insight', 'kableExtra',
  'parameters', 'performance', 'tables', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'broom.mixed', 'estimatr', 'flextable', 'fixest', 'gamlss',
  'ggplot2', 'gt', 'huxtable', 'knitr', 'lme4', 'lmtest', 'officer',
  'rmarkdown', 'sandwich', 'testthat', 'vdiffr', 'spelling'

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modeltime', 'modeltime.resample', 'tune', 'rsample', 'yardstick',
  'workflows', 'parsnip', 'recipes', 'dials', 'timetk', 'tibble',
  'dplyr', 'tidyr', 'purrr', 'glue', 'stringr', 'rlang', 'cli',
  'crayon', 'generics', 'magrittr', 'glmnet', 'progressr', 'tictoc'

Packages suggested but not available for checking:
  'roxygen2', 'earth', 'testthat', 'tidymodels', 'xgboost',
  'tidyverse', 'lubridate', 'knitr', 'rmarkdown', 'covr', '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:
  'modeltime', 'parsnip', 'timetk', 'magrittr', 'rlang', 'reticulate',
  'tibble', 'forcats', 'dplyr', 'tidyr', 'purrr', 'stringr', 'glue',
  'fs'

Packages suggested but not available for checking:
  'tidyverse', 'tidymodels', '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:
  'modeltime', 'h2o', 'magrittr', 'rlang', 'tibble', 'timetk', 'dplyr',
  'parsnip', 'purrr', 'tidyr', 'stringr', 'glue', 'fs'

Packages suggested but not available for checking:
  'tidymodels', 'workflows', 'tidyverse', 'knitr', 'rmarkdown',
  'roxygen2', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'StanHeaders', 'timetk', 'parsnip', 'dials', 'yardstick',
  'workflows', 'hardhat', 'rlang', 'glue', 'plotly', 'reactable', 'gt',
  'ggplot2', 'tibble', 'tidyr', 'dplyr', 'purrr', 'stringr', 'forcats',
  'scales', 'janitor', 'progressr', 'magrittr', 'forecast', 'xgboost',
  'prophet', 'cli'

Packages suggested but not available for checking:
  'rstan', 'slider', 'tidymodels', 'recipes', 'rsample', 'tune',
  'tidyverse', 'lubridate', 'progress', 'testthat', 'roxygen2',
  'kernlab', 'earth', 'randomForest', 'tidyquant', 'knitr',
  'rmarkdown', 'webshot', '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:
  'modeltime', 'tune', 'rsample', 'workflows', 'parsnip', 'recipes',
  'dials', 'yardstick', 'timetk', 'tibble', 'dplyr', 'tidyr', 'purrr',
  'forcats', 'glue', 'stringr', 'ggplot2', 'plotly', 'cli', 'crayon',
  'magrittr', 'rlang', 'progressr', 'tictoc'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'tidymodels', 'tidyverse', 'tidyquant',
  'glmnet', 'lubridate', 'knitr', 'rmarkdown', 'covr', 'remotes'

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'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'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:
  'magrittr', 'dplyr', 'ggplot2', 'tibble', 'janitor', 'broom',
  'formula.tools', 'stringr', 'knitr', 'infer', 'rlang', 'glue'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'vdiffr', 'ggplot2movies',
  'openintro', 'patchwork', 'viridis', 'readr'

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: 'markovchain', '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:
  'knitr', 'rhandsontable', 'shiny', '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:
  'shiny', 'DT', 'shinydashboard', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'norm'

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:
  'date', 'sp', 'sfsmisc', 'raster', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mapdata', 'raster', 'bitops', 'curl', 'devtools', 'mapedit', 'maps',
  'maptools', 'ptw', 'rgdal', 'rgeos', 'sf', 'sp'

Package suggested but not available for checking: 'tinytest'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'testthat', 'rgdal', 'ggplot2', '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:
  'assertthat', 'bitops', 'data.table', 'gdalUtilities', 'geojsonio',
  'httr', 'jsonlite', 'raster', 'sf', 'stringr', 'xml2', 'xts'

Packages suggested but not available for checking:
  'dplyr', 'DT', 'formatR', 'geojsonlint', 'ggplot2', 'httptest',
  'knitr', 'leafem', 'leaflet', 'magrittr', 'mapedit', 'png',
  'rappdirs', 'rgdal', 'rmarkdown', 'shiny', 'shinyalert',
  'shinydashboard', 'shinyFiles', 'shinyjs', 'spelling', 'testthat',
  'tibble', 'tidyr', 'xtable'

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', 'sandwich', 'AER'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'AER'
Running examples in 'modmarg-Ex.R' failed
The error most likely occurred in:

> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
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: 'gtools', 'igraph'

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

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

Package suggested but not available for checking: 'rgl'

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:
  'jmuOutlier', 'ellipse', 'hypergeo', 'gsl'

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

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

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

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

Packages suggested but not available for checking:
  'smoof', 'scatterplot3d', 'irace', 'testthat', 'knitr', 'rmarkdown',
  'emoa', 'ggplot2', 'reshape2', '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:
  'matrixStats', 'mclust', 'mvnfast', 'vcd'

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

VignetteBuilder 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', 'glue', 'purrr', 'httr', 'jsonlite', 'tibble', 'readr',
  'rlang', 'stringr', 'assertthat', 'cli', 'dplyr', 'lubridate'

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: 'VGAM', 'tolerance'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RJSONIO', 'magrittr', 'tidyr', 'iterators', 'stringr', 'compareDF'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DiceKriging', 'GenSA', 'emoa', 'mco', 'GPareto'

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

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

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

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

VignetteBuilder 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', 'urltools', 'xml2', 'aws.iam', 'aws.s3', 'MolgenisAuth',
  'arrow'

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

VignetteBuilder 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', 'urltools'

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pander', 'dplyr', 'testthat', '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:
  'mvtnorm', 'ncvreg', 'Rcpp', 'mclust', 'RcppArmadillo'

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

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

Packages suggested but not available for checking:
  'lmtest', 'knitr', 'texreg'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/gelS4.Rnw'
   'inst/doc/gmmS4.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
agostino.test: no visible global function definition for
  'complete.cases'
agostino.test: no visible global function definition for 'pnorm'
anscombe.test: no visible global function definition for
  'complete.cases'
anscombe.test: no visible global function definition for 'pnorm'
bonett.test: no visible global function definition for 'complete.cases'
bonett.test: no visible global function definition for 'pnorm'
jarque.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'numDeriv', 'CircStats', 'crawl',
  'mitools', 'car', 'mvtnorm', 'sp', 'Brobdingnag', 'nleqslv',
  'qdapRegex', 'geosphere', 'prodlim', 'doRNG', 'data.tree',
  'extraDistr', 'rlang', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'setRNG', 'splines2', 'R.rsp', 'raster', 'conicfit',
  'ggplot2', 'ggmap', 'lubridate', 'dplyr', 'magrittr',
  'scatterplot3d', 'BB', 'expm', 'matrixcalc', 'moveHMM'

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:
  'dendextend', 'dplyr', 'magrittr', 'geometry', 'geomorph', 'ggplot2',
  'jpeg', 'progress', 'RColorBrewer', 'rgeos', 'sp', 'vegan', 'tibble'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown', 'rmarkdown', 'aricode', 'ggplot2',
  'tidytext', '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: 'Hmisc', 'gplots', 'nortest'

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

Packages suggested but not available for checking: 'TTmoment', 'tmvtnorm'

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

Package suggested but not available for checking: 'sass'

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

Packages suggested but not available for checking: 'DT', 'shiny', 'shinyBS'

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

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

Packages suggested but not available for checking:
  'spelling', 'nycflights13', 'ggplot2'

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

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

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

Packages suggested but not available for checking: 'fftw', 'RODBC', 'knitr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'dplyr', 'foreach', 'ggplot2', 'permute', 'purrr',
  'rlang', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'mice', 'rmarkdown', 'covr', '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:
  'maptools', 'circular', 'png', 'raster', 'rmarkdown', 'sp'

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:
  'compare', 'doParallel', 'foreach', 'iterators', 'sitar'

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

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

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

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

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

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

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: 'lavaan'

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:
  'DBI', 'dplyr', 'ggplot2', 'tidytext', 'ggwordcloud', 'stringr',
  'rlang', 'scales', 'RMariaDB', 'glue', 'config', 'anytime', 'here',
  'cli', 'lifecycle', 'RSQLite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettyunits', '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:
  'nortest', 'sjmisc', 'stringr', 'magrittr', 'ztable'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'sjlabelled', '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: 'scatterplot3d'
mopsocd : initialize_pop: no visible global function definition for
  'runif'
mopsocd : compute_velocity: no visible global function definition for
  'runif'
mopsocd : mutate: 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: 'psych', 'gplots', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkTH: no visible global function definition for 'pchisq'
getOrderPval: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'party', 'partykit', 'varImp', 'plyr', 'foreach', 'measures', 'iml',
  'pdp', 'vip', 'ggplot2', 'rlang'

Packages suggested but not available for checking:
  'doParallel', 'knitr', 'rmarkdown', 'rmdformats', 'GDAtools',
  'RColorBrewer', 'caret', 'pROC', 'tidyverse', 'e1071'

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'
ametrine : <anonymous>: no visible global function definition for
  'approx'
ametrine: no visible global function definition for 'rgb'
isolum : <anonymous>: no visible global function definition for
  'approx'
isolum: no visible global function definition for 'rgb'
morgenstemning : <anonymous>: no visible global function definition for
  'approx'
morgenstemning: 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
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: 'jointDiag', 'pracma'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Arothron', 'Rvcg', 'Morpho', 'oce', 'rgdal', 'raster', 'sp',
  'geometry', 'rgl', 'colorRamps', 'DescTools'

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

Packages suggested but not available for checking:
  'car', 'shapes', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
cor.gen: no visible global function definition for 'rnorm'
cor.gen: no visible global function definition for 'resid'
cor.gen: no visible global function definition for 'lm'
cor.gen: no visible binding for global variable 'sd'
cor.gen: no visible global function definition for 'cor'
cor.gen: no visible global function definition for 'write.table'
stat.gen: no visible global function definition for 'rexp'
stat.gen: no visible global function definition for 'rnorm'
stat.gen: no visible binding for global variable 'sd'
stat.gen: no visible global function definition for 'write.table'
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'coda', 'deSolve', 'dplyr', 'epitools', 'ggplot2', 'gridExtra',
  'magrittr', 'reshape2', 'rjags', 'tibble', 'tidyr', '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:
  'magrittr', 'Rdpack', 'reshape2', 'crayon', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyr', 'dplyr', 'ggplot2',
  'RCurl'

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

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

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:
  'minpack.lm', 'RCurl', 'pbapply', '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.
Packages required but not available: 'ggplot2', 'scales', 'pracma'

Packages suggested but not available for checking:
  'knitr', 'tidyverse', 'rmarkdown', 'reshape2'

Packages which this enhances but not available for checking:
  'MortalityLaws', 'lifecontingencies'

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: 'wpp2017'

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

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

VignetteBuilder 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', 'tidyr'

Packages suggested but not available for checking:
  'mosaicData', 'mosaic', 'ggformula', 'NHANES', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mosaic', 'reshape2', 'ggplot2', 'dplyr', 'tidyr', 'ggformula'
Note: found 7 marked UTF-8 strings
Running examples in 'mosaicData-Ex.R' failed
The error most likely occurred in:

> ### Name: HeatX
> ### Title: Data from a heat exchanger laboratory
> ### Aliases: HeatX
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # We can test for heat exchange with the environment by checking to see if the 
> # heat gained by the cold water matches the heat lost by the hot water.
> C_p <- 4.182 / 60  # / 60 because measuring m in L/min
> HeatX2 <- 
+   dplyr::mutate(HeatX,
+     Q.cold = m.cold * C_p * (T.cold.out - T.cold.in),
+     Q.hot  = m.hot * C_p * (T.hot.out- T.hot.in),
+     Q.env  = Q.cold + Q.hot
+   )
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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:
  'mosaicCore', 'dplyr', 'caret', 'ggplot2', 'ggformula', 'lazyeval',
  'knitr', 'testthat', 'tibble', 'tidyr', 'tidyverse'

Packages suggested but not available for checking:
  'mosaic', 'mosaicData', 'randomForest'

VignetteBuilder 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', 'ggformula', 'mosaicData', 'mosaicCore', 'ggplot2',
  'ggstance', 'ggridges', 'ggrepel', 'rlang', 'tidyr', 'readr',
  'latticeExtra', 'ggdendro', 'gridExtra', 'glue', 'broom', 'leaflet'

Packages suggested but not available for checking:
  'vdiffr', 'lubridate', 'magrittr', 'NHANES', 'RCurl', 'sp',
  'maptools', 'vcd', 'testthat', 'knitr', 'mapproj', 'rgl',
  'rmarkdown', 'covr', 'formatR', 'palmerpenguins'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ecr', 'BBmisc', 'checkmate', 'ParamHelpers', 'smoof', 'mlrCPO',
  'mlr', 'parallelMap'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'magrittr', 'testthat', 'praznik', 'mlrMBO',
  'emoa', 'DiceKriging', 'rgenoud', 'randomForest', 'digest'

VignetteBuilder 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', 'assertthat', 'pracma', 'NlcOptim', 'nloptr', 'sfsmisc'

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: 'dbscan', 'Rtsne'

Packages suggested but not available for checking:
  'annotate', 'bigparallelr', 'bigstatsr', 'clValid', 'ComplexHeatmap',
  'fpc', 'ggplot2', 'ggpmisc', 'ggthemes', 'gridExtra', 'irlba',
  'knitr', 'rmarkdown', 'testthat', 'viridis'

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: 'RColorBrewer', 'plot3D', 'Rcpp'

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

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

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'mclust', '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:
  'comat', 'philentropy', 'Rcpp', 'sf', 'stars', 'tibble',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'spdep', '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', 'ggplot2', 'ggraph', 'igraph', 'intergraph', 'network',
  'purrr', 'RColorBrewer', 'reshape2', 'reticulate', 'rlang', 'scales',
  'tibble', 'tidygraph'

Packages suggested but not available for checking:
  'ergm', 'knitr', 'pkgdown', 'rmarkdown', '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:
  'ape', 'Rcpp', 'coda', 'ks', 'mvtnorm', 'caper'

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

VignetteBuilder 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', 'dygraphs'

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: 'Formula'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pracma', 'dplyr', 'tidyr', 'magrittr', 'ggplot2', 'scales', 'psych',
  'Rcpp', 'diptest', 'RColorBrewer', 'cstab', 'fastcluster', 'fields',
  'rlang'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CircStats', 'Rcpp', 'sp', 'geosphere', 'ggplot2', 'ggmap',
  'numDeriv', 'RcppArmadillo'

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/moveHMM-custom-plots.Rnw'
   'inst/doc/moveHMM-guide.Rnw'
   'inst/doc/moveHMM-starting-values.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geosphere', 'sp', 'raster', 'rgdal', 'httr', 'memoise', 'xml2',
  'Rcpp'

Packages suggested but not available for checking:
  'adehabitatHR', 'adehabitatLT', 'markdown', 'rmarkdown', 'circular',
  'ggmap', 'mapproj', 'maptools', 'testthat', 'knitr', 'ggplot2',
  'leaflet', 'lubridate', 'ctmm', 'amt', 'bcpa', 'EMbC'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'move', 'raster', 'sf', 'lwgeom', 'slippymath', 'lubridate', 'curl',
  'ggplot2', 'cowplot', 'magick', 'gifski', 'av', 'pbapply', 'magrittr'

Packages suggested but not available for checking:
  'mapview', 'leaflet', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'move', '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: 'skmeans', 'clue', 'slam'

Packages suggested but not available for checking:
  'tm', 'vcd', 'SnowballC', 'HSAUR3', 'colorspace',
  'corpus.useR.2008.abstracts', 'flexmix'

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:
  'R.utils', 'changepoint', 'glmnet', 'HDPenReg', 'spikeslab'

Packages suggested but not available for checking:
  'CGHcall', 'aroma.affymetrix', 'aroma.cn', 'aroma.core',
  'aroma.light', 'snowfall', 'R.devices', 'R.filesets', 'R.methodsS3',
  'R.oo', 'matrixStats'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'pamr', 'pscl', 'numDeriv', 'foreach', 'doParallel', 'bst',
  'WeightSVM'

Packages suggested but not available for checking:
  'zic', 'R.rsp', 'knitr', 'rmarkdown', 'gdata', 'e1071', 'SparseM',
  'slam'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlbench', 'bayesm', 'cvTools', 'mlogit'

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:
  'knitr', 'pinp', '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', 'ggpubr', 'generics', 'tibble', 'dplyr', 'rlang',
  'stringr', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'spelling', 'covr', 'markdown',
  'tidyverse', 'modelsummary', 'broom'

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.
Package unavailable to check Rd xrefs: 'lme4'
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: 'car', 'purrr'

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: 'BiasedUrn'

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

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running examples in 'MPkn-Ex.R' failed
The error most likely occurred in:

> ### Name: MPkn-package
> ### Title: Calculations of One Discrete Model in Several Time Steps
> ### Aliases: MPkn-package
> 
> ### ** Examples
> 
> require(MPkn)
> require(markovchain)
Loading required package: markovchain
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'markovchain'
> options(digits = 14)
> n = 12
> k = 2
> rz = 11
> P = array(0, c(rz, rz))
> for (i in 1:rz){
+   po = runif(rz)
+   P[i, ] = po/sum(po)
+ }
> I = diag(1, rz, rz)
> Myy = MUPkL(P, P, I, n, k, c(1:rz))
> StSy = NULL
> for (i in 1:rz) StSy = c(StSy, Myy$Navg[,,i][n])
> mrkv = new("markovchain", transitionMatrix = P)
Error in getClass(Class, where = topenv(parent.frame())) : 
  "markovchain" is not a defined class
Calls: new -> getClass
Execution halted
Packages required but not available:
  'leaps', 'foreach', 'bestglm', 'doParallel', 'doRNG', 'plyr',
  'shinydashboard', 'shiny', 'glmnet', 'googleVis', 'ggplot2',
  'reshape2', 'scales', 'dplyr', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'gsubfn', 'coda', 'xtable', 'texreg', 'pander', 'digest',
  'ggplot2', 'data.table', 'rlang'

Packages suggested but not available for checking:
  'rhdf5', 'relimp', 'testthat'

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

Package suggested but not available for checking: 'lavaan'

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.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'KernSmooth' 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  'packageDescription'
export.summary.mpm: no visible global function definition for
  'write.table'
mpm: no visible binding for global variable 'median'
plot.mpm: no visible global function definition for 'rainbow'
plot.mpm: no visible global function definition for 'quantile'
plot.mpm: no visible global function definition for 'par'
plot.mpm: no visible global function definition for 'points'
plot.mpm: no visible global function definition for 'smoothScatter'
plot.mpm: no visible global function definition for 'colorRampPalette'
plot.mpm: no visible global function definition for 'symbols'
plot.mpm: no visible global function definition for 'text'
plot.mpm: no visible global function definition for 'lines'
plot.mpm: no visible global function definition for 'box'
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
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:
  'stringr', 'stringi', 'partitions', 'plyr', 'ggplot2', 'polynom',
  'orthopolynom', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
place: no visible global function definition for 'points'
plot,mproc: no visible binding for global variable 'rainbow'
plot,mproc: no visible global function definition for 'plot.default'
plot,mproc: no visible global function definition for 'axis'
plot,mproc: no visible global function definition for 'points'
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'qtl', '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: 'Rcpp', 'RcppArmadillo'

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.
Package required but not available: 'ape'

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

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

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

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:
  'numDeriv', 'Brobdingnag', 'Rcpp', 'RcppEigen'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'tidyr', 'dplyr', 'tibble', 'rlang', 'reshape2',
  'ggplot2', 'MPTinR', 'TreeBUGS', 'runjags', 'coda', 'purrr', 'readr',
  'limSolve'

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', 'sp', 'animation', 'zoo', 'rasterVis', 'latticeExtra',
  'viridis'

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

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'

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

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

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: 'mvtnorm', 'multcomp', 'survPresmooth'

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

Packages suggested but not available for checking:
  'testthat', 'rjags', 'tidyverse', 'knitr', 'ggplot2', 'ggmcmc',
  'DescTools', 'bayesmeta', 'kableExtra', 'roxygen2', 'bookdown',
  'MendelianRandomization'

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

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: 'tables'

Package suggested but not available for checking: 'geepack'

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

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:
  'httr', 'jsonlite', 'xml2', 'wellknown', 'rappdirs', 'sp',
  'data.table', 'tibble'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'geojsonio', 'rgdal', 'rgeos', 'knitr',
  'rmapshaper'

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

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.
Malformed Description field: should contain one or more complete sentences.
densityfn: no visible global function definition for 'dnbinom'
densityfn: no visible global function definition for 'dpois'
densityfn: no visible global function definition for 'dgeom'
form.add: no visible global function definition for 'formula'
mreg: no visible global function definition for 'model.frame'
mreg: no visible global function definition for 'model.response'
mreg: no visible global function definition for 'model.matrix'
mreg: no visible global function definition for 'model.offset'
mreg: no visible global function definition for 'nlm'
paper: no visible global function definition for 'model.matrix'
randfn: no visible global function definition for 'rnbinom'
randfn: no visible global function definition for 'rpois'
randfn: no visible global function definition for 'rgeom'
randfn: no visible global function definition for 'rbinom'
summary.mreg: no visible global function definition for 'pnorm'
summary.mreg: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'dplyr', 'tidyr', 'ggplot2', 'Rdpack', 'RcppArmadillo'

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

VignetteBuilder 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', 'glmnet', 'grplasso', 'plyr', 'randtoolbox', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'purrr', 'plyr', 'ggplot2', 'dplyr', 'caret', 'gridExtra',
  'magrittr', 'reshape2', 'sfsmisc', 'igraph', 'pbapply'

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', 'abind', 'geometry', 'matrixStats', 'reshape2',
  'RcppEigen', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'robustbase'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mrgsolve', 'withr', 'purrr', 'dplyr', 'assertthat', 'rlang',
  'ggplot2', 'tidyselect', 'tidyr', 'tibble', 'patchwork'

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', 'dplyr', 'magrittr', 'tibble', 'rlang', 'tidyselect',
  'lifecycle', 'glue', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'testthat', 'xml2', 'rmarkdown', 'yaml', 'knitr', 'data.table',
  'pmxTools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'KMsurv', '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: 'misc3d', 'oro.nifti'

Package suggested but not available for checking: 'tkrplot'

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:
  'shiny', 'lars', 'Rcpp', 'foreach', 'ncvreg', 'coin', 'shinyjs',
  'data.table', 'doParallel', 'sampling', 'bigmemory', 'mrMLM', 'sbl',
  'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lars', 'Rcpp', 'foreach', 'ncvreg', 'coin', 'sampling',
  'data.table', 'doParallel', 'sbl', 'RcppEigen'

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:
  'lubridate', 'reshape2', 'ggplot2', 'lmtest', 'plyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bnlearn', 'compositions', 'dynamicTreeCut', 'GGally', 'fastcluster',
  'gtools', 'graph', 'Hmisc', 'mice', 'network', 'pcalg', 'psych',
  'Rgraphviz', 'sna', 'WGCNA', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'R6', 'stringr', 'stringi', 'magrittr', 'assertthat',
  'base64enc', '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.
Package required but not available: 'nortest'

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

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: 'Rcpp', 'data.table'

Package suggested but not available for checking: 'testthat'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'visNetwork', '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: 'Rcpp', 'igraph', 'RcppArmadillo'

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', '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.
Package required but not available: 'magic'

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:
  'glmnet', 'ncvreg', 'foreach', 'mvtnorm'

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

Packages suggested but not available for checking:
  '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: 'magic'

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

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

Packages suggested but not available for checking:
  'Biostrings', '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:
  'stringr', 'crayon', 'xml2', 'reshape2', 'ggplot2', 'ggfortify',
  'plotly'

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: 'Rcpp', 'RcppParallel'

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', 'officer', 'cellranger', 'writexl', 'xml2', 'htmltools'

Package suggested but not available for checking: 'tinytest'

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

Packages suggested but not available for checking:
  'Synth', 'DEoptim', 'rgenoud', 'DEoptimR', 'GenSA', 'GA', 'soma',
  'cmaes', 'Rmalschains', 'NMOF', 'nloptr', 'hydroPSO', 'pso',
  'LowRankQP', 'kernlab', 'reshape', '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: 'plyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'phangorn', 'RandomFieldsUtils', 'zipfR', 'Rdpack', 'foreach',
  'doParallel'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'mscsweblm4r'

VignetteBuilder 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', 'tuneR'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'testthat', 'rvest', 'xml2', 'zoo'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'mscstexta4r'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cv.msda: no visible global function definition for 'predict'
formatoutput: no visible global function definition for 'new'
msda.prep: no visible global function definition for 'cov'
plot.msda: no visible global function definition for 'par'
plot.msda: no visible global function definition for 'matplot'
plot.msda: no visible global function definition for 'rainbow'
plot.msda: no visible global function definition for 'approx'
plot.msda: no visible global function definition for 'axis'
predict.msda: no visible binding for global variable 'sd'
predict.msda: no visible global function definition for 'predict'
zeromat: no visible global function definition for 'new'
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'sde', 'moments', 'mvtnorm'

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', 'RcppArmadillo', 'RcppProgress'

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:
  'snowfall', 'abind', 'dplyr', 'ggplot2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'broom', 'covr', 'crayon', 'devtools', 'DT', 'fmsb', 'ggrepel',
  'gridExtra', 'kableExtra', 'knitr', 'openxlsx', 'purrr', 'r4ss',
  'readxl', 'reshape2', 'rfishbase', 'rmarkdown', 'shiny', 'testthat',
  'tidyr'

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

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

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

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

Packages suggested but not available for checking:
  'animation', 'igraph', 'maps', 'mvtnorm', 'rgl', 'RgoogleMaps',
  'plotrix', 'ggplot2', 'sna'

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', 'covr'

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

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: 'doParallel', 'foreach'

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

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

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

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

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: 'mvtnorm', 'expm'

Packages suggested but not available for checking:
  'mstate', 'minqa', 'doParallel', 'foreach', 'numDeriv', 'testthat',
  'flexsurv'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nleqslv', 'ggplot2', 'ggpubr', 'foreach', 'iterators', 'doParallel'

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: 'gtools', 'reshape2', 'dplyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'lubridate', 'magrittr', 'progress', 'purrr',
  'rlang', 'sjlabelled', 'stringr', 'tidyselect', 'tidytable', 'tidyr'

Packages suggested but not available for checking:
  'haven', 'tibble', '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: 'RODBC'

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

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

Packages suggested but not available for checking: 'KMsurv', 'Rgraphviz'

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

Packages suggested but not available for checking:
  'cmprsk', 'ggplot2', '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: 'knitr', 'rmarkdown'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'expm', 'PP', 'mirt', 'scDIFtest', 'eRm'

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

VignetteBuilder 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', 'latex2exp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'doParallel', 'nls2', 'RColorBrewer', 'plotrix'

Packages suggested but not available for checking:
  'RSQLite', '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: '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: 'Formula', 'partykit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'crul', 'openssl', 'jsonlite', 'data.table', 'R6',
  'rstudioapi', 'shinyjs', 'shiny'

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

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', 'sf', 'cartography'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ineq', 'png', 'reshape2'

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'

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', 'XML', 'stringr', 'plyr', 'dplyr', 'ggplot2',
  'magrittr', 'lubridate', 'tidyr', 'dtw', 'proxy'

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.
Packages suggested but not available for checking: 'ggplot2', 'car'
'LazyData' is specified without a 'data' directory
Running examples in 'mthapower-Ex.R' failed
The error most likely occurred in:

> ### Name: mthapower
> ### Title: Power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Packages required but not available:
  'stringr', 'XML', 'sensitivity', 'lhs', 'rgl'

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:
  'ggplot2', 'reshape2', 'testthat', 'vdiffr', '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: 'glmnet', 'e1071'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', '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:
  'magrittr', 'png', 'jpeg', 'tiff', 'bmp', 'magick', 'imager', 'dplR',
  'spatstat.geom', 'measuRing', 'shiny', 'dplyr', 'shinydashboard',
  'shinyWidgets'

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

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: 'Rcpp', 'fGarch', 'fBasics', 'mvtnorm'

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: 'epiDisplay', 'ggplot2', 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 2632 marked UTF-8 strings
Packages required but not available:
  'ggplot2', 'dplyr', 'jsonlite', 'tibble', 'magrittr', 'stringr',
  'readr', 'tidyr', 'lubridate', 'rlang', 'tidyselect', 'withr',
  'glue', 'fs'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'ggplot2', 'zoo', 'reshape2', 'broom', 'dplyr'

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: 'DiceKriging'

Package suggested but not available for checking: 'rgenoud'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deldir', 'splancs', 'sp', 'conf.design', 'Hmisc', 'dplyr', 'purrr',
  'gtools', 'magrittr', 'plyr', 'polyclip', 'rgeos', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'geozoo', 'plotly', '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: 'DiagrammeR', 'dplyr', 'stringr'

Package suggested but not available for checking: 'htmlwidgets'

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

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: 'gtools', 'digest'

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:
  'scales', 'geometry', 'deldir', 'mirt', 'GPArotation', 'optimr',
  'Hmisc', 'car', 'dunn.test', 'gplots', 'polycor', 'dae', 'rgl',
  'xtable', 'mvtnorm'

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

Packages suggested but not available for checking:
  'lme4', 'robustbase', 'coin', 'xtable', 'lmtest', 'coxme', 'SimComp',
  'ISwR', 'tram'

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

> ### Name: multcompBoxplot
> ### Title: boxplot with multcomp graphics
> ### Aliases: multcompBoxplot
> ### Keywords: aplot
> 
> ### ** Examples
> 
> 
> # Example from help("TukeyHSD")
> multcompBoxplot(breaks~tension, data=warpbreaks)
> # 'sortFn' can be either a function or a function name
> # default order is 'decreasing=TRUE'
> multcompBoxplot(breaks~tension, data=warpbreaks,
+        sortFn=median, decreasing=FALSE)
> 
> ##################
> library(multcomp)
Error in library(multcomp) : there is no package called 'multcomp'
Execution halted
Package required but not available: 'MTS'

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

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: 'SimComp'
multeq.diff: no visible global function definition for 'cov'
multeq.diff: no visible global function definition for 'pt'
multeq.diff: no visible global function definition for 'qt'
multeq.rat: no visible global function definition for 'cov'
multeq.rat: no visible global function definition for 'pt'
multeq.rat: no visible global function definition for 'qt'
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gnm', 'VGAM'

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

VignetteBuilder 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', 'plyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
synthetic_multiband: no visible global function definition for 'runif'
synthetic_multiband: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'RcppParallel', 'BH'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'MCMCpack', 'ggplot2',
  'matrixStats', 'plotrix'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgl', 'tkrplot', 'tcltk2', 'shapes', 'dendroextras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Brobdingnag', 'coda', 'mvtnorm', 'purrr', 'Rcpp', 'magrittr',
  'progress', 'Rdpack', '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: 'bitops', 'multcomp'

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', 'plotly', 'shiny', 'shinythemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ranger', 'Boruta', 'dunn.test', 'caret', 'e1071', 'rdist'

Packages suggested but not available for checking:
  'BiocManager', 'Biobase', 'switchBox', 'knitr', 'rmarkdown',
  'BiocStyle', 'leukemiasEset', '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: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
calculate_direction: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'cowsay', 'crayon', 'dplyr', 'glue', 'magrittr', 'purrr', 'stringi',
  'stringr', 'tibble', 'tidyr'

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

VignetteBuilder 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', 'abind', 'foreach', 'mvtnorm', 'sciplot'

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: 'nbpMatching', 'crossmatch'

Package suggested but not available for checking: 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'lme4', 'pcaMethods', 'misc3d', 'RColorBrewer',
  'gridGraphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'crayon', 'dplyr', 'magrittr', 'qs', 'R6', 'rlang',
  'tibble', 'vctrs'

Packages suggested but not available for checking:
  'covr', 'knitr', 'lubridate', 'nycflights13', 'rmarkdown',
  'testthat', 'vroom'

VignetteBuilder 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', 'ez', 'stringr', 'reshape2', 'tibble', 'ggplot2',
  'effsize', 'BayesFactor', 'bayestestR', 'broom', 'effectsize', 'esc',
  'forestplot', 'bootstrap'

Packages suggested but not available for checking:
  'gridExtra', 'fastDummies', 'vctrs', 'tidyselect', 'tidyr', 'plyr',
  'ggraph', 'igraph', 'testthat', 'cowplot', 'covr'

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

Packages suggested but not available for checking:
  'png', 'qgraph', '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: 'ellipse', 'imager', 'agricolae'

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: 'mvtnorm', 'fastGHQuad'

Package suggested but not available for checking: 'testthat'

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

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

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: 'ape', 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'xtable', 'PSAgraphics', 'plyr', 'psych', 'reshape',
  '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:
  'lme4', 'lmerTest', 'data.table', 'extraoperators', 'JWileymisc',
  'cowplot', 'ggplot2', 'lavaan', 'zoo'

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:
  'sys', 'fs', 'usethis', 'zip', 'askpass', 'xml2', 'rvest',
  'rstudioapi'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'statmod', 'RMark', 'Brobdingnag', 'mvtnorm', 'prodlim',
  'sp', 'raster'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'nor1mix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
multinb.fit: no visible global function definition for 'nlminb'
multinbmod: no visible global function definition for 'is.empty.model'
multinbmod: no visible global function definition for 'model.matrix'
multinbmod: no visible binding for global variable 'contrasts'
multinbmod: no visible global function definition for 'model.response'
multinbmod: no visible global function definition for 'model.offset'
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
Packages required but not available: 'igraph', 'Rcpp', 'RColorBrewer'

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

Packages suggested but not available for checking:
  'sand', 'statnet', 'data.table', 'testthat', 'igraphdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'Rdpack', 'tibble',
  'dplyr', 'rlang', 'purrr', 'forcats', 'glue', 'randtoolbox',
  'copula', 'tidyr', 'stringr', 'igraph', 'ggraph', 'ggplot2',
  'ggdist', 'truncdist', 'bayesplot', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'R.rsp', 'rprojroot', 'loo',
  'logitnorm', 'crayon', 'tidygraph', 'pkgdown'

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', 'Rglpk', 'quadprog', 'coda', 'RcppXPtrUtils',
  'RcppArmadillo', 'RcppProgress'

Packages suggested but not available for checking:
  'rPorta', 'knitr', '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: 'rgenoud', '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.
Packages required but not available:
  'assertive.base', 'assertive.files', 'assertive.numbers',
  'assertive.properties', 'assertive.types', 'ggplot2', 'gridGraphics',
  'gtable', 'magick', 'magrittr', 'stringi'

Packages suggested but not available for checking:
  'ComplexHeatmap', 'roxygen2', 'VennDiagram', '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:
  'abind', 'epitools', 'meta', 'HardyWeinberg', 'RColorBrewer'

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

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'multigraph', 'Rgraphviz', 'knitr', 'rmarkdown'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/TwoModeNetworks.Rnw'
(Is a VignetteBuilder field missing?)
Package unavailable to check Rd xrefs: 'multigraph'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/TwoModeNetworks.Rnw'
(Is a VignetteBuilder field missing?)
Package required but not available: 'lpSolveAPI'

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

Package suggested but not available for checking: 'polynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
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: 'pROC', 'risksetROC', 'snowfall'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'SuppDists', 'quantreg'
Package unavailable to check Rd xrefs: 'quantreg'
Running examples in 'MultiRobust-Ex.R' failed
The error most likely occurred in:

> ### Name: MR.quantile
> ### Title: Multiply Robust Estimation of the Marginal Quantile
> ### Aliases: MR.quantile
> 
> ### ** Examples
> 
> # Simulated data set
> set.seed(123)
> n <- 400
> gamma0 <- c(1, 2, 3)
> alpha0 <- c(-0.8, -0.5, 0.3)
> X <- runif(n, min = -2.5, max = 2.5)
> p.mis <- 1 / (1 + exp(alpha0[1] + alpha0[2] * X + alpha0[3] * X ^ 2))
> R <- rbinom(n, size = 1, prob = 1 - p.mis)
> a.x <- gamma0[1] + gamma0[2] * X + gamma0[3] * exp(X)
> Y <- rnorm(n, a.x, sd = sqrt(4 * X ^ 2 + 2))
> dat <- data.frame(X, Y)
> dat[R == 0, 2] <- NA
> 
> # Define the outcome regression models and missingness probability models
> imp1 <- glm.work(formula = Y ~ X + exp(X), family = gaussian)
> imp2 <- glm.work(formula = Y ~ X + I(X ^ 2), family = gaussian)
> mis1 <- glm.work(formula = R ~ X + I(X ^ 2), family = binomial(link = logit))
> mis2 <- glm.work(formula = R ~ X + exp(X), family = binomial(link = cloglog))
> MR.quantile(response = Y, tau = 0.25, imp.model = list(imp1, imp2),
+             mis.model = list(mis1, mis2), L = 10, data = dat)
Error in MR.quantile(response = Y, tau = 0.25, imp.model = list(imp1,  : 
  need CRAN package 'quantreg' for quantile estimation
Execution halted
Packages required but not available: 'zoo', 'magrittr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

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: 'sensitivity', 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'statmod', 'psych', 'ggplot2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CCM_boot : <anonymous>: no visible global function definition for 'sd'
SSR_check_signal: no visible global function definition for 'cor'
SSR_check_signal: no visible global function definition for 'cor.test'
SSR_check_signal: no visible global function definition for 'lm'
SSR_pred_boot: no visible global function definition for 'cor'
make_ccm_data: no visible global function definition for 'rnorm'
make_ccm_data: no visible global function definition for 'runif'
make_ccm_data: no visible global function definition for 'rlnorm'
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
Package required but not available: 'reshape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'psd', 'astrochron', 'fftwtools', 'slp'
Packages required but not available: 'igraph', 'Rcpp', 'microbenchmark'

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', 'bootstrap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BinOrdNonNor', 'CorrToolBox', 'corpcor', 'moments', 'norm',
  'PoisNonNor'

Package suggested but not available for checking: 'PoisBinOrdNonNor'

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: 'glmnet'

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: 'emulator', 'mvtnorm'

Package suggested but not available for checking: 'abind'

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

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

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

Package suggested but not available for checking: 'lmtest'

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

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

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:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'

Depends: includes the non-default packages:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'
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 suggested but not available for checking:
  'lme4', 'gamm4', 'geepack'

Packages which this enhances but not available for checking:
  'aod', 'aods3', 'betareg', 'caper', 'coxme', 'cplm', 'gee', 'glmmML',
  'logistf', 'MCMCglmm', 'ordinal', 'pscl', 'spdep', 'spatialreg',
  'splm', 'unmarked', 'geeM', 'gamlss'
Packages unavailable to check Rd xrefs: 'AICcmodavg', 'bbmle', 'glmulti', 'arm', 'gee', 'geepack', 'geeM', 'wgeesel', 'ape', 'bestglm', 'leaps', 'lme4', 'cplm', 'gamm4', 'gamlss', 'glmmML', 'glmmTMB', 'MCMCglmm', 'pscl', 'aod', 'aods3', 'betareg', 'brglm', 'spatialreg', 'splm', 'coxme', 'quantreg', 'ordinal', 'logistf', 'caper', 'maxlike', 'RMark'
Packages required but not available:
  'lme4', 'TMB', 'Rcpp', 'stringr', 'RcppEigen'

Package suggested but not available for checking: 'knitr'

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

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

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

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

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

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

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

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

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

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', 'magrittr', 'qmap', 'lubridate'

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: 'seewave'

Package suggested but not available for checking: 'plsgenomics'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'DescTools', 'pander'
Packages required but not available: 'digest', 'formatR', 'qs', 'tibble'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
prentice.test: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available:
  'mutoss', 'multcomp', 'plotrix', 'rJava', 'JavaGD', 'CommonJavaJars',
  'JGR'

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

Packages suggested but not available for checking:
  'fdrtool', 'qvalue', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Familias', 'paramlink', 'expm', 'IBDsim'

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

Packages suggested but not available for checking:
  'dplyr', 'reshape2', 'kableExtra', '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: 'sm', 'gtools'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'HSAUR2'

Packages suggested but not available for checking:
  'mvtnorm', 'mclust', 'flexclust', 'RLRsim', 'multcomp', 'ape', 'sem',
  'scatterplot3d'

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', 'RcppArmadillo'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Formula', 'MNM', 'quantreg', 'Rfit', 'SpatialNP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'dummies', 'ggplot2', 'moments', 'penalized', 'plyr',
  'reshape2', 'sn'

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:
  'Rdpack', 'WeightIt', 'cobalt', 'matrixNormal', 'geometry', 'sp',
  'gbm', 'CBPS'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'dagitty', 'ggdag', '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: 'car', 'heplots'

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'
Package required but not available: 'CompQuadForm'

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: 'fields', 'wavethresh', 'xts', 'zoo'

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

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

Packages suggested but not available for checking:
  'metafor', 'meta', 'rmeta', 'dlnm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BMS', 'dplyr', 'lazyeval', 'plyr', 'rlang', 'xts', 'zoo',
  'robustbase'

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:
  'phytools', 'ape', 'corpcor', 'subplex', 'spam', 'glassoFast',
  'pbmcapply'

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

VignetteBuilder 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', 'plyr'

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

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:
  'knitr', 'rmarkdown', 'testthat', 'mvtnorm', 'microbenchmark',
  'plyr', 'RhpcBLASctl'

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

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

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
mvnpermute: no visible global function definition for 'lm'
mvnpermute: no visible global function definition for 'coef'
mvnpermute: no visible global function definition for 'resid'
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
Packages required but not available:
  'nortest', 'moments', 'robustbase', 'mvoutlier', 'plyr', 'psych',
  'energy', 'kableExtra', 'magrittr', 'car'

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/MVN.Rnw'
(Is a VignetteBuilder field missing?)

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

Package suggested but not available for checking: 'markdown'

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

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:
  'minqa', 'BB', 'ucminf', 'dfoptim', 'pbivnorm', 'optimx', 'mnormt',
  'numDeriv'

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

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

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spray', 'microbenchmark', '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', 'maxLik', 'abind', 'bayesm', 'miscTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
mvorpb: no visible global function definition for 'pnorm'
mvorpb: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
Packages required but not available: 'data.table', 'statmod'

Packages suggested but not available for checking:
  'knitr', 'rgl', '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: 'plotrix'

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: 'Rcpp', 'RcppArmadillo', 'RcppThread'

Packages suggested but not available for checking:
  'dplyr', 'furrr', 'knitr', 'rmarkdown', 'stringr', 'testthat',
  'textmineR', 'tidytext', 'spelling'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
rtn: no visible global function definition for 'runif'
rtn: no visible global function definition for 'qnorm'
rtn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'abind', 'ape', 'mvtnorm', 'matrixcalc', 'ouch', 'PCMBase', 'TreeSim'

Packages suggested but not available for checking:
  'PCMBaseCpp', 'geiger', 'ggplot2', 'knitr', 'rdryad', '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: 'MCMCpack', 'mvtnorm', 'mnormt'

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.
Package suggested but not available for checking: 'heavy'
Package required but not available: 'RColorBrewer'

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

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

Packages suggested but not available for checking:
  'fracdiff', '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 suggested but not available for checking: 'penalized'
Running examples in 'MWLasso-Ex.R' failed
The error most likely occurred in:

> ### Name: MWLasso
> ### Title: Penalized Moving-Window Lasso Method for Genome-Wide Association
> ###   Studies
> ### Aliases: MWLasso MW_parameters
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> # In example 1, feature matrix X and response variable Y are randomly generated.
> # Example 1:
> n = 100
> p = 200
> X = matrix(rnorm(n*p, mean = 0, sd = 1), nrow = n, ncol = p)
> X[2,1] = NA; X[80:90,1]= NA; 
> Y =  rnorm(n, mean = 0, sd = 1)
> 
> number = 20
> gamma2 = 0.1
> d = 4
> params = MW_parameters(X, Y, d, number, gamma2, method="linear")
Tuning parameters are: lambda = 0.1413146, eta = 1.271831.> lambda = params[1]
> eta = params[2]
> beta.hat = MWLasso(X, Y, lambda, eta, d, method="linear")
> 
> # In example 2, the nki70 dataset is from the "penalized" package
> # (https://cran.r-project.org/web/packages/penalized/penalized.pdf).
> # The response variable Y is "event", the disease indicator.
> # The feature matrix X is "TSPYL5...C20orf46", the gene expression
> # measurements of 70 prognostic genes.
> # Example 2:
> require("penalized")
Loading required package: penalized
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'penalized'
> data(nki70)
Warning in data(nki70) : data set 'nki70' not found
> data = nki70
Error: object 'nki70' not found
Execution halted
Package required but not available: 'glmnet'

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: 'shiny', 'htmltools'

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', '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:
  'ordinal', 'quantreg', 'lme4', 'foreach', 'doParallel', 'relations',
  'Rfast', 'visNetwork', 'energy', 'geepack', 'knitr', 'dplyr',
  'bigmemory', 'coxme', 'Rfast2', 'Hmisc'

Packages suggested but not available for checking: 'markdown', '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 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.
abcpred_nmer: no visible global function definition for 'write.table'
algpred: no visible global function definition for 'read.table'
algpred: no visible global function definition for 'write.table'
allermatch: no visible global function definition for 'read.table'
allermatch: no visible global function definition for 'write.table'
bcepred_nmer: no visible global function definition for 'write.table'
bimas_nmer: no visible global function definition for 'write.table'
filter.firstlayer: no visible global function definition for
  'read.table'
filter.firstlayer: no visible global function definition for
  'write.table'
iedb_arb_mhci_nmer: no visible global function definition for
  'write.table'
iedb_arb_mhcii_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhci_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhcii_nmer: no visible global function definition for
  'write.table'
netmhcNN_nmer: no visible global function definition for 'write.table'
netmhcWT_nmer: no visible global function definition for 'write.table'
propred_nmer: no visible global function definition for 'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
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 required but not available: 'XML'

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: 'Myrrixjars', 'rJava'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'nortest', 'fitdistrplus', 'foreach', 'doParallel', 'dplyr',
  'RColorBrewer', 'taxize', 'reshape2', 'ggplot2', 'readr', 'tibble',
  'scales', 'gridExtra', 'edgeR', 'RcppArmadillo', 'cpp11'

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

Package suggested but not available for checking: 'lme4'

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', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'rvest', 'httr', 'jsonlite', 'tidyr', 'tibble', 'dplyr',
  '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: 'Rcpp', 'RcppSpdlog', '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: 'data.table', 'stringi'

Packages suggested but not available for checking:
  'devtools', 'httr', 'jsonlite', 'magrittr', 'testthat', 'ISOcodes',
  'xml2', 'rmarkdown', 'roxygen2', 'rvest'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'crayon', 'dplyr', 'ggbeeswarm', 'ggforce', 'ggplot2',
  'ggrepel', 'knitr', 'magrittr', 'purrr', 'rlang', 'rmarkdown',
  'rstudioapi', 'scales', 'sessioninfo', 'shiny', 'shinyWidgets',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'covr', 'Biobase', 'GEOquery', 'limma'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'EnvStats', 'fitdistrplus', 'Kendall', 'multcomp', 'NADA', 'perm',
  'survminer', 'cenGAM', 'vegan', 'coin'

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:
  'mlr3', 'mlr3pipelines', 'paradox', 'mlr3learners', 'missForest',
  'missMDA', 'doParallel', 'testthat', 'Amelia', 'VIM', 'softImpute',
  'missRanger', 'mice', 'data.table', 'foreach', 'glmnet'

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

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:
  'MCMCglmm', 'asreml'
Package unavailable to check Rd xrefs: 'MCMCglmm'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'RColorBrewer', 'magrittr', 'mapdata', 'maps', 'rgdal', 'rlang',
  'lifecycle'

Packages suggested but not available for checking:
  'covr', 'knitr', 'readxl', '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
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/intro_naivebayes.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/intro_naivebayes.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'grpreg', 'gmm', 'ncvreg', 'glmnet'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'data.table', 're2r', 'knitr', 'rmarkdown', 'rex',
  'dplyr', 'tidyr', 'rematch2'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'data.table'
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: 'Biostrings'
Package unavailable to check Rd xrefs: 'Biostrings'
Packages required but not available:
  'fs', 'glue', 'magrittr', 'purrr', 'tibble', 'dplyr', 'rstudioapi'

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

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: 'Rcpp'

Package suggested but not available for checking: '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:
  'knitr', 'rmarkdown', 'bWGR'

VignetteBuilder 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', 'autothresholdr', 'BBmisc', 'checkmate', 'detrendr',
  'dplyr', 'filesstrings', 'ggplot2', 'glue', 'ijtiff', 'magrittr',
  'purrr', 'Rcpp', 'reshape2', 'rlang', 'stringr', 'viridis', 'withr'

Packages suggested but not available for checking:
  'abind', 'covr', 'gridExtra', 'knitr', 'matrixStats', 'pacman',
  '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:
  'dplyr', 'ggplot2', 'purrr', 'tidyr', 'tibble', 'magrittr', 'visdat',
  'rlang', 'forcats', 'viridis', 'glue', 'UpSetR'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'rpart.plot', 'covr', 'gridExtra',
  'wakefield', 'vdiffr', 'here', 'simputation', 'imputeTS', 'gdtools',
  'Hmisc', '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: 'distrEx', 'rgl'

Packages suggested but not available for checking: 'DEoptim', 'mco'

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

Packages suggested but not available for checking:
  'googleVis', 'lme4', 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'ccaPP', 'dplyr', 'epiR', 'magrittr', 'purrr', '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.
Packages required but not available:
  'bit64', 'RcppCCTZ', 'zoo', 'Rcpp', 'RcppDate'

Packages suggested but not available for checking:
  'tinytest', 'data.table', 'xts'

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

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:
  'strucchange', 'tseries', 'Formula', 'gtools', 'car'

Package suggested but not available for checking: 'testthat'

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

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: 'plyr', 'dplyr', 'png', 'jsonlite'

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

Packages suggested but not available for checking:
  'apsimx', 'ggplot2', 'knitr', 'purrr', 'terra', 'rmarkdown',
  'rnaturalearth', '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:
  'Rdpack', 'rdist', 'stabledist', 'beepr'

Packages suggested but not available for checking:
  'ppclust', 'spatialClust', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'rvest', 'xml2', 'magrittr', 'dplyr', 'tidyr', 'readxl',
  'lubridate', 'zoo', 'stringr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gh', 'remotes', 'usethis', 'curl', 'withr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgl', 'nat', 'nabor', 'dendroextras', 'plyr', 'spam'

Packages suggested but not available for checking:
  'spelling', 'bigmemory', 'ff', '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:
  'rgl', 'nabor', 'igraph', 'filehash', 'digest', 'nat.utils', 'plyr',
  'yaml'

Packages suggested but not available for checking:
  'Rvcg', 'testthat', 'httr', 'XML', 'knitr', 'rmarkdown',
  'alphashape3d'

VignetteBuilder 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', 'tibble'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nat', 'rgl', 'digest', 'igraph', 'memoise', 'rappdirs'

Packages suggested but not available for checking:
  'spelling', 'git2r', 'nabor', 'testthat', 'covr'

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

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 'issue-1.R'
Running the tests in 'tests/issue-1.R' failed.
Complete output:
  > stopifnot(require(testthat))
  Loading required package: testthat
  Error: require(testthat) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  Execution halted
Packages required but not available: 'knitr', 'tuneR'

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 suggested but not available for checking: 'testthat', '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
Packages suggested but not available for checking: 'hypergeo', 'testthat'
Package unavailable to check Rd xrefs: 'CBPS'
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', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'plyr', 'rvest', 'stringr', '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: 'dplyr'

Package suggested but not available for checking: 'ggplot2'

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

Packages suggested but not available for checking: 'BiocGenerics', 'DEXSeq'

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: 'PWEALL'

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'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NB.estimator: no visible global function definition for 'optimize'
NB.estimator: no visible global function definition for 'uniroot'
NB.example.dataset: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  optimize uniroot write.table
Consider adding
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
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:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

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

Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'igraph', 'knitr', 'pheatmap', 'RColorBrewer',
  '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: 'drc', 'gdata', 'kyotil', 'gWidgets2'

Packages suggested but not available for checking:
  'knitr', 'RUnit', 'rjags', '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:
  'scales', 'gtable', 'knitr', 'xtable', 'reshape2', 'dplyr', 'Cairo',
  'readr', 'lazyeval', 'PopED', 'magrittr', 'rlang', 'purrr', 'tibble',
  'rmarkdown', 'tidyr', 'ggplot2', 'gridExtra', 'bookdown'

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:
  'gplots', 'quantreg', 'sfa', 'lpSolve', 'ggplot2', 'doParallel',
  'foreach', 'iterators', 'plotly'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ncbit : FUN: no visible global function definition for 'read.table'
ncbit : FUN: no visible global function definition for 'head'
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
Packages required but not available: 'ncdf4', 'PCICt', 'abind'

Packages suggested but not available for checking: 'proj4', 'testthat'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'pkgdown', 'sp', 'geoknife',
  'ncdf4', '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: 'dplyr', 'ncdf4'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
d0: no visible global function definition for 'qnorm'
dncgamma: no visible global function definition for 'dpois'
indncgamma: no visible global function definition for 'pgamma'
indncgamma: no visible global function definition for 'dpois'
inxncgamma: no visible global function definition for 'qnorm'
inxncgamma: no visible global function definition for 'pgamma'
inxncgamma: no visible global function definition for 'dpois'
pncgamma: no visible global function definition for 'pgamma'
pncgamma: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'rlang', 'RNetCDF', 'tibble', 'tidyr'

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: 'proftools'

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

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

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

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:
  'downloader', 'ggplot2', 'jsonlite', 'RColorBrewer'

Packages suggested but not available for checking:
  'cowplot', 'dplyr', 'DT', 'ggplotify', 'maps', 'magick', 'shiny',
  'shinyBS', 'shinydashboard', 'shinycssloaders', 'remotes', 'plotly',
  'prettydoc', 'knitr', 'rmarkdown', 'reshape2', 'ggrepel',
  'shadowtext', '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: 'Rcpp', 'RcppArmadillo'

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', 're2r', 'stringi', 'ggplot2', 'tidyr', 'cdata',
  'reshape2', 'knitr', 'markdown', 'R.utils'

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

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

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:
  'Rcpp', 'glmnet', 'mvtnorm', 'fields', '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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ashr', 'knitr', 'rmarkdown', 'tinytest'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'Rcpp', 'data.table', 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'network', 'networkDynamic', 'animation', 'sna', 'statnet.common',
  'jsonlite', 'base64'

Packages suggested but not available for checking:
  'tergm', 'tsna', 'testthat', 'knitr', 'htmlwidgets', 'scatterplot3d'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', '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: '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:
  'PoweR', 'plyr', 'bayestestR', 'pROC', 'MBESS', 'car', 'ez',
  'BayesFactor', 'Exact', 'ggplot2', 'ggpubr', 'logspline'

Package suggested but not available for checking: 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rtweet', 'randomForest', 'stringr', 'SnowballC', 'SparseM', 'tau',
  'tm'

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', 'combinat'
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Running 'run_tests.R'
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'msm', 'bit'

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: 'roxygen2'
Packages required but not available:
  'magrittr', 'RDStreeboot', 'igraph', 'RDS', 'dplyr'

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', 'mlbench'

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: 'optimbase', 'optimsimplex'

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

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

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:
  'attempt', 'data.table', 'glue', 'httr', 'igraph', 'jsonlite',
  'magrittr', 'purrr', 'R6', 'rlang', 'rstudioapi', 'shiny', 'tibble',
  'tidyr', 'tidyselect'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'zoo', 'downloader', 'httr', 'jsonlite', 'lubridate',
  'neonUtilities', 'magrittr', 'rhdf5', 'R.utils', 'tidyselect',
  'data.table', '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:
  'DBI', 'duckdb', 'httr', 'progress', 'R.utils', 'thor', 'vroom',
  'zip'

Packages suggested but not available for checking:
  'tibble', 'jsonlite', 'testthat', 'covr', 'xml2', 'spelling',
  'rstudioapi', 'neonUtilities', 'rhdf5', 'curl', 'openssl', 'digest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'httr', 'jsonlite', 'downloader', 'data.table', 'R.utils',
  'readr', 'tidyr', 'stringr', 'pbapply', 'curl'

Packages suggested but not available for checking:
  'rhdf5', 'raster', 'sp', 'testthat', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'reshape2', 'jsonlite', 'httr', 'xml2', 'analogue',
  'leaflet', 'dplyr'

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: 'igraph', 'PairedData'

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

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

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

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

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', 'rlang', 'vctrs', 'tidyselect'

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', 'infotheo', 'corpcor', 'huge', 'vegan'

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

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

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: 'igraph', 'haven'

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

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: 'gdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clue', 'expm', 'igraph', 'pdist', 'pracma', 'vegan'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'sna', 'network', 'networkDynamic', 'MatchIt', 'SparseM',
  'igraph', 'viridisLite', 'RcppArmadillo'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'qtl', 'glasso', 'RBGL', 'huge', 'tmvtnorm'

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: 'LIM'
EnvInd: 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:
  'ggplot2', 'igraph', 'brainGraph', '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.
Packages required but not available:
  'raster', 'abind', 'car', 'CircStats', 'data.table', 'Hmisc',
  'matrixStats', 'plyr', 'quickPlot', 'sp', 'SpaDES.tools', 'rgeos'

Packages suggested but not available for checking:
  'fastshp', 'knitr', 'magrittr', 'microbenchmark', 'rmarkdown', 'sf',
  'SpaDES.core', '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: 'meta', 'magic', 'ggplot2', 'metafor'

Packages suggested but not available for checking:
  'colorspace', 'rgl', 'hasseDiagram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive', 'devtools', 'dplyr', 'rappdirs', 'readr', 'seqinr',
  'stringr', 'testit', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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:
  'clue', 'gtools', 'igraph', 'lda', 'poisbinom', 'Rcpp',
  'RcppArmadillo'

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

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

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

Package suggested but not available for checking: 'bionetdata'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'magrittr', 'ggplot2', 'testthat', 'shiny',
  'miniUI', 'rstudioapi'

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', 'knitcitations'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'foreach', 'Rcpp', 'statmod', 'RhpcBLASctl', 'abind', 'RColorBrewer',
  'BH', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bigmemory', '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', 'magrittr', 'wTO', 'CoDiNA', 'dplyr', 'Rfast', 'binr'

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.
Packages required but not available:
  'DiagrammeR', 'DiagrammeRsvg', 'htmlwidgets', 'knitr', 'magrittr',
  'rsvg', 'svglite', 'png', 'segmented', 'gtools'

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'crch', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'igraph'

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

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: 'RColorBrewer', 'network', 'sna'

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:
  'MCMCpack', 'ggplot2', 'Rmpfr', 'abind', 'mvtnorm', 'tidyr', 'sna',
  'igraph', 'qgraph', 'network', 'RColorBrewer', 'reshape', 'ggrepel',
  'gridExtra', 'rlang', 'GGally', 'ggvis'

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:
  'qgraph', 'IsingFit', 'IsingSampler', 'reshape2'

Package suggested but not available for checking: 'networktools'

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

Packages suggested but not available for checking: 'htmltools', 'jsonlite'

Packages which this enhances but not available for checking:
  'knitr', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'Rdpack', 'RSpectra', 'doParallel', 'foreach', 'graphon',
  'igraph', 'network', 'pracma', '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: 'networkDynamic', 'network'

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

Package suggested but not available for checking: 'testthat'

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

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

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:
  'Rcpp', 'assertthat', 'checkmate', 'ggplot2', 'ggrepel',
  'RcppProgress'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'pander', 'igraph', '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: 'tibble', 'magrittr'

Packages suggested but not available for checking:
  'sna', 'statnet.common', 'testthat', 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'functional', 'ggplot2', 'lazyeval', 'plyr', 'reshape2', 'stringr',
  'dplyr', 'surveybootstrap'

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: 'expm', 'ggplot2', 'dplyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'igraph', 'KFAS', 'limSolve', 'plyr', 'Rglpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'psych', 'corrplot', 'fdrtool', 'R.matlab', 'igraph', 'qgraph',
  'ppcor', 'foreach', 'doParallel', 'pwr', 'IsingFit', 'pbapply'

Package suggested but not available for checking: 'googledrive'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qgraph', 'igraph', 'IsingFit', 'reshape2', 'ggplot2', 'gridExtra',
  'NetworkComparisonTest', 'cocor', 'RColorBrewer', 'R.utils',
  'eigenmodel', 'psych', 'smacof', 'wordcloud'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partykit', 'qgraph', 'mvtnorm', 'Formula', 'gridBase', 'reshape2'

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

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

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', 'scales', 'tidyr'

Packages suggested but not available for checking:
  'caret', 'neuralnet', 'RSNNS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
mlptrain : rect: no visible global function definition for 'polygon'
mlptrain : drawnet: no visible global function definition for 'title'
mlptrain : drawnet: no visible global function definition for 'polygon'
mlptrain : drawnet: no visible global function definition for 'text'
mlptrain : drawnet: no visible global function definition for 'lines'
mlptrain: no visible global function definition for 'runif'
mlptrain: no visible global function definition for 'locator'
mlptrain: no visible global function definition for 'polygon'
mlptrain: no visible global function definition for 'text'
rbftrain : rect: no visible global function definition for 'polygon'
rbftrain : drawnet: no visible global function definition for 'title'
rbftrain : drawnet: no visible global function definition for 'polygon'
rbftrain : drawnet: no visible global function definition for 'text'
rbftrain : drawnet: no visible global function definition for 'lines'
rbftrain : graph: no visible global function definition for 'title'
rbftrain : graph: no visible global function definition for 'polygon'
rbftrain : graph: no visible global function definition for 'text'
rbftrain : graph: no visible global function definition for 'lines'
rbftrain : graph: no visible global function definition for 'points'
rbftrain: no visible global function definition for 'runif'
rbftrain: no visible global function definition for 'locator'
rbftrain: no visible global function definition for 'polygon'
rbftrain: no visible global function definition for 'text'
rbftrain: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans lines locator points polygon runif text title
Consider adding
  importFrom("graphics", "lines", "locator", "points", "polygon", "text",
             "title")
  importFrom("stats", "kmeans", "runif")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'gridExtra', 'NeuralNetTools', 'reshape2', 'caret',
  'fastDummies', 'stringr', 'Hmisc', 'ggforce', 'scales', 'ggnewscale'

Packages suggested but not available for checking:
  'h2o', 'neural', 'RSNNS', 'neuralnet', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'oro.nifti', 'abind', 'matrixStats', 'R.utils', 'RNifti'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'knitr', 'rmarkdown', 'dplyr', 'reshape2',
  'httr', 'covr', 'brainR'

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', 'knitr', 'rmarkdown', '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:
  'digest', 'httr', 'xml2', 'base64enc', 'aws.s3'

Packages suggested but not available for checking:
  'dplyr', '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:
  'stringr', 'hash', 'yaImpute', 'Rcpp', 'iterators', 'abind',
  'assertthat', 'readr', 'rgl'

Packages suggested but not available for checking:
  'foreach', '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:
  'BayesLogit', 'ggplot2', 'dplyr', 'tidyr', 'magrittr', 'gridExtra'

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.
Packages required but not available:
  'dplyr', 'ggplot2', 'scales', 'pracma', 'ggpmisc', 'cowplot'

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: 'xts', 'zoo'

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

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

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

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:
  'devtools', 'httr', 'jsonlite', 'tidyr', 'xml2', 'lubridate',
  'askpass'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'magrittr', 'rmarkdown', 'robotstxt', 'rvest',
  'stringr', 'testthat', 'mockery', 'tidytext', 'textdata'

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: 'tidyRSS'

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:
  'quanteda', 'quanteda.textstats', 'stringi'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'desc', 'knitr', 'lintr', '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: 'psych'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
nfca : nFCAmain: no visible global function definition for 'hist'
nfca : nFCAmain: no visible global function definition for
  'flush.console'
nfca : nFCAmain: no visible global function definition for 'qnorm'
nfca : nFCAmain: no visible global function definition for 'read.csv'
nfca : nFCAmain: no visible global function definition for 'cor'
nfca : nFCAmain: no visible global function definition for 'as.dist'
nfca : nFCAmain: no visible global function definition for 'cophenetic'
nfca : nFCAmain: no visible global function definition for 'hclust'
nfca : thresholdTEST: no visible global function definition for
  'read.csv'
nfca : gScript: no visible global function definition for 'read.csv'
nfca : gScript0: no visible global function definition for 'read.csv'
nfca : gMatrix: no visible global function definition for 'read.csv'
nfca: no visible global function definition for 'cor'
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Running examples in 'nFCA-Ex.R' failed
The error most likely occurred in:

> ### Name: nfca
> ### Title: Numerical Formal Concept Analysis for Systematic Clustering
> ### Aliases: nfca
> 
> ### ** Examples
> 
> # View a build-in correlation matrix: nfca_example
> data("nfca_example", package = "nFCA")
> nfca_example
      H    W    S    D   HF   HM   WF   WM   H1   W1    O
1  1.00 0.95 0.90 0.90 0.85 0.85 0.80 0.80 0.40 0.30 0.10
2  0.95 1.00 0.88 0.88 0.70 0.70 0.87 0.87 0.20 0.45 0.15
3  0.90 0.88 1.00 0.82 0.80 0.80 0.76 0.76 0.10 0.10 0.02
4  0.90 0.88 0.82 1.00 0.82 0.82 0.81 0.81 0.10 0.10 0.05
5  0.85 0.70 0.80 0.82 1.00 0.95 0.65 0.65 0.08 0.06 0.01
6  0.85 0.70 0.80 0.82 0.95 1.00 0.60 0.60 0.06 0.07 0.01
7  0.80 0.87 0.76 0.81 0.65 0.60 1.00 0.95 0.03 0.05 0.01
8  0.80 0.87 0.76 0.81 0.65 0.60 0.95 1.00 0.01 0.02 0.01
9  0.40 0.20 0.10 0.10 0.08 0.06 0.03 0.01 1.00 0.02 0.01
10 0.30 0.45 0.10 0.10 0.06 0.07 0.05 0.02 0.02 1.00 0.02
11 0.10 0.15 0.02 0.05 0.01 0.01 0.01 0.01 0.01 0.02 1.00
>      
> # 1. using the default 'histogram' method and choosing threshold
> # automatically   
> nfca(data = nfca_example)
Warning in system("ruby multistagefca.rb") : 'ruby' not found
Warning in file.rename("example.dot", "example.txt") :
  cannot rename file 'example.dot' to 'example.txt', reason 'The system cannot find the file specified'
Warning in file(file, "rt") :
  cannot open file 'example.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: nfca ... thresholdTEST -> as.matrix -> read.csv -> read.table -> file
Execution halted
Packages required but not available:
  'FKF.SP', 'LSMRealOptions', 'numDeriv', 'rgenoud', 'mathjaxr',
  'Rdpack', 'curl'

Packages suggested but not available for checking:
  'OptionPricing', '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', 'glue', 'httr', 'janitor', 'jsonlite', 'magrittr',
  'nflfastR', 'purrr', 'stringr', 'tibble', 'tidyr', 'tidyselect',
  'xgboost'

Packages suggested but not available for checking:
  'future', 'gt', 'rmarkdown', 'tictoc', 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'curl', 'dplyr', 'fastrmodels', 'furrr', 'future', 'glue',
  'janitor', 'lubridate', 'lifecycle', 'magrittr', 'progressr',
  'rlang', 'stringr', 'tibble', 'tidyr', 'tidyselect', 'usethis',
  'xgboost'

Packages suggested but not available for checking:
  'crayon', 'DBI', 'DT', 'gsisdecoder', 'httr', 'jsonlite', 'purrr',
  'qs', 'rmarkdown', 'RSQLite', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'crayon', 'curl', 'dplyr', 'furrr', 'future', 'glue',
  'gsubfn', 'magrittr', 'progressr', 'purrr', 'readr', 'rlang',
  'tibble', 'tidyr'

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

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

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:
  'graph', 'igraph', 'stringr', 'magrittr', 'plyr', 'ggplot2',
  'apcluster', 'KEGGgraph', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'graphite', 'NFPdata', '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', 'gsl', 'lamW'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running examples in 'NFWdist-Ex.R' failed
The error most likely occurred in:

> ### Name: nfw
> ### Title: The Standard Distribution Functions for the 3D NFW Profile
> ### Aliases: NFW NFWdist nfw dnfw pnfw qnfw rnfw
> ### Keywords: nfw
> 
> ### ** Examples
> 
> #Both the PDF (dnfw) integrated up to x, and CDF at q (pnfw) should be the same:
> #0.373, 0.562, 0.644, 0.712
> 
> for(con in c(1,5,10,20)){
+   print(integrate(dnfw, lower=0, upper=0.5, con=con)$value)
+   print(pnfw(0.5, con=con))
+ }
[1] 0.373455
[1] 0.373455
[1] 0.5618349
[1] 0.5618349
[1] 0.6437556
[1] 0.6437556
[1] 0.7116174
[1] 0.7116174
> 
> #The qnfw should invert the pnfw, returning the input vector (1:9)/10:
> for(con in c(1,5,10,20)){
+   print(qnfw(p=pnfw(q=(1:9)/10,con=con), con=con))
+ }
Using slow internal Lambert W0, ideally you shouls install the lamW or the gsl package.
Package required but not available: 'Rfast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'httr', 'rlang', 'RCurl', 'dplyr', 'cli', 'tibble', 'tidyr', 'rjson',
  'stringr', 'ggplot2', 'scales', 'xml2', 'textutils', 'lifecycle'

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'batchmeans', '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:
  'mvtnorm', 'fields', 'dlm', 'car', 'interp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'Hmisc', 'rvest', 'magrittr', 'xml2', '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 suggested but not available for checking: 'mosaic'
Packages required but not available:
  'dplyr', 'sf', 'RANN', 'units', 'magrittr', 'jsonlite', 'httr',
  'igraph', 'xml2', 'R.utils', 'tidyr', 'rosm', 'prettymapr', 'fst',
  'dataRetrieval', 'rappdirs', 'zip'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'markdown', 'ggmap', 'ggplot2',
  'sp', 'lwgeom', 'devtools', '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:
  'maps', 'rappdirs', 'rgdal', 'sf', 'httr', 'rvest', 'xml2',
  'ggplot2', 'gdalUtils', 'rlang', 'dplyr', 'curl', 'units', 'stringr',
  'memoise', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'wikilake', 'sp', 'rgeos', 'testthat', 'covr',
  'crul'

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: 'jsonlite'

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:
  'httr', 'jsonlite', 'RSQLite', 'rvest', 'DBI', '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:
  'BayesLogit', 'msm', 'MCMCpack', 'Rcpp'

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

Package suggested but not available for checking: 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ucminf', 'lars', 'glasso', 'ncvreg'

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.
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
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'caret', 'e1071', 'readr', 'magrittr', 'varhandle',
  'rsample', 'ggplot2', 'lme4', 'ModelMetrics', 'lmtest', 'rmarkdown',
  'scales', 'ggrepel', 'lubridate', 'tidyr', 'forcats', 'knitr',
  'janitor', 'stringi', 'synthpop'

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'

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'

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:
  'ape', 'castor', 'concaveman', 'geiger', 'raster', 'rgdal', 'rgeos',
  'sf', 'sp', 'stringr'

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

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

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'

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: 'lpSolve', 'TSP'
Packages required but not available:
  'assertthat', 'ggplot2', 'ggthemes', 'scales', 'gtools', 'dplyr',
  'gridExtra'

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

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

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.
Packages required but not available: 'igraph', 'coda', '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: 'nimble'

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

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
Packages required but not available: 'bbw', 'withr'

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

Package suggested but not available for checking: 'RColorBrewer'

Packages which this enhances but not available for checking:
  'kokudosuuchi', 'estatapi', 'jpndistrict', 'jpmesh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rsamtools', 'sets', 'S4Vectors'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Packages required but not available: 'fdasrvf', 'fda', 'fda.usc'

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', 'dplyr', 'RCurl', 'jsonlite'

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: 'zoo', 'car'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plyr', 'reshape2', 'ggplot2', 'scales',
  'MuMIn', '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: 'bpcp', 'ssanv'

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

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

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

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

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: 'rappdirs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'magrittr', 'skimr', 'sf', 'maps',
  'R.rsp'

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: 'quadprog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'a4Core', 'MLInterfaces', 'xtable', 'limma', 'Biobase', 'multtest',
  'RColorBrewer', 'pamr', 'randomForest', 'ROCR', 'ipred', 'e1071',
  'kernlab'

Packages suggested but not available for checking: 'RUnit', 'ALL'

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

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

VignetteBuilder 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', 'timeSeries', 'Rdpack'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'chk', 'coda', 'extras', 'generics', 'lifecycle', 'purrr',
  'term', 'tibble', 'universals'

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

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.
Package suggested but not available for checking: 'Hmisc'
Packages suggested but not available for checking:
  'reshape', 'WWGbook', 'ellipse', 'roxygen2', 'testthat'
Malformed Title field: should not end in a period.
Pwr.lme: no visible global function definition for 'anova'
Pwr.lme: no visible global function definition for 'qf'
Pwr.lme: no visible global function definition for 'pf'
logLik1.lme: no visible global function definition for 'coef'
logLik1.lme: no visible global function definition for 'model.matrix'
logLik1.lme: no visible global function definition for 'predict'
logLik1.lme: no visible global function definition for 'formula'
runScript: no visible binding for global variable 'example'
sigmaTolme: no visible global function definition for 'vcov'
simulateY.lme: no visible global function definition for 'runif'
simulateY.lme: no visible global function definition for 'fitted'
simulateY.lme: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Running 'Pwr1.R'
Running the tests in 'tests/Pwr1.R' failed.
Complete output:
  > date()
  [1] "Sun Apr 25 12:47:58 2021"
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'brew', 'lbfgsb3c', 'dparser', 'ggplot2', 'rex', 'minqa',
  'n1qn1', 'fastGHQuad', 'RxODE', 'magrittr', 'backports', 'symengine',
  'RcppEigen', 'BH', 'StanHeaders', 'RcppArmadillo'

Packages suggested but not available for checking:
  'Deriv', 'Rvmmin', 'broom.mixed', 'crayon', 'knitr', 'data.table',
  'devtools', 'digest', 'dotwhisker', 'dplyr', 'expm', 'flextable',
  'ggtext', 'patchwork', 'gridExtra', 'huxtable', 'lbfgs', 'lotri',
  'madness', 'matrixcalc', 'nloptr', 'officer', 'pkgdown', 'reshape2',
  'rmarkdown', 'testthat', 'tidyr', 'ucminf', 'vpc', 'xgxr', 'yaml',
  'xpose', 'generics', 'tibble', 'checkmate', 'cli', 'qs', 'covr',
  'forecast', 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lqmm', 'HI', 'mvtnorm', 'numDeriv', 'statmod', 'Qtools', 'Rcpp',
  'RcppArmadillo', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'minpack.lm', 'optimx', 'Rvmmin', 'Rcgmin', 'numDeriv'
Running examples in 'nlmrt-Ex.R' failed
The error most likely occurred in:

> ### Name: model2grfun
> ### Title: Generate a gradient function from a nonlinear model expression
> ###   and a vector of named parameters.
> ### Aliases: model2grfun
> ### Keywords: nonlinear least squares
> 
> ### ** Examples
> 
>   cat("See also examples in nlmrt-package.Rd\n")
See also examples in nlmrt-package.Rd
>   require(numDeriv)
Loading required package: numDeriv
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'numDeriv'
>   y <- c(5.308, 7.24, 9.638, 12.866, 17.069, 23.192, 31.443, 38.558, 
+       50.156, 62.948, 75.995, 91.972)  # for testing
>   tt <- seq_along(y)  # for testing
>   f <- y ~ b1/(1 + b2 * exp(-1 * b3 * tt))
>   p <- c(b1 = 1, b2 = 1, b3 = 1)
>   mygr <- model2grfun(f, p)
>   myss <- model2ssfun(f, p) # for check
>   cat("mygr:\n")
mygr:
>   print(mygr)
function (prm, y = NULL, tt = NULL) 
{
    b1 <- prm[[1]]
    b2 <- prm[[2]]
    b3 <- prm[[3]]
    localdf <- data.frame(y, tt)
    jstruc <- with(localdf, eval({
        .expr4 <- exp(-1 * b3 * tt)
        .expr6 <- 1 + b2 * .expr4
        .expr11 <- .expr6^2
        .value <- b1/.expr6 - y
        .grad <- array(0, c(length(.value), 3), list(NULL, c("b1", 
            "b2", "b3")))
        .grad[, "b1"] <- 1/.expr6
        .grad[, "b2"] <- -(b1 * .expr4/.expr11)
        .grad[, "b3"] <- b1 * (b2 * (.expr4 * tt))/.expr11
        attr(.value, "gradient") <- .grad
        .value
    }))
    jacmat <- attr(jstruc, "gradient")
    resids <- as.numeric(eval(b1/(1 + b2 * exp(-1 * b3 * tt)) - 
        y))
    grj <- as.vector(2 * crossprod(jacmat, resids))
}
<environment: 0x0000000013246470>
>   
>   ans <- mygr(p, tt = tt, y = y)
>   print(ans)
[1] -824.042084    4.764888  -11.025384
>   gnum <- grad(myss, p, tt = tt, y = y)
Error in grad(myss, p, tt = tt, y = y) : could not find function "grad"
Execution halted
Errors in running code in vignettes:
when running code in 'nlmrt-vignette.Rnw'
  ...
> require(optimx)
Loading required package: optimx
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'optimx'

> aopx <- optimx(st, shobbs.f, shobbs.g, control = list(all.methods = TRUE))

  When sourcing 'nlmrt-vignette.R':
Error: could not find function "optimx"
Execution halted

  'nlmrt-vignette.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'nlmrt-vignette.Rnw' using Sweave
Loading required package: nlmrt
Error in nlsModel(formula, mf, start, wts, scaleOffset = scOff, nDcentral = nDcntr) : 
  singular gradient matrix at initial parameter estimates
Error in nls(regmod, start = huetstart, trace = FALSE, data = pastured) : 
  singular gradient
Loading required package: optimx
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'optimx'

Error: processing vignette 'nlmrt-vignette.Rnw' failed with diagnostics:
 chunk 10 (label = chunk10) 
Error in optimx(st, shobbs.f, shobbs.g, control = list(all.methods = TRUE)) : 
  could not find function "optimx"

--- failed re-building 'nlmrt-vignette.Rnw'

SUMMARY: processing the following file failed:
  'nlmrt-vignette.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ROCR', 'TSP', 'igraph', 'fdrtool', 'coin', 'earth', 'randomForest',
  'e1071'

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', 'inline'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'NLP', 'xml2', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'udpipe', 'spacyr', 'cleanNLP'
Packages unavailable to check Rd xrefs: 'tm', 'udpipe', 'spacyr', 'cleanNLP'
Packages required but not available:
  'data.table', 'SuperLearner', 'cvAUC', 'ROCR', 'Rdpack', 'bde', 'np',
  'assertthat'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'prettydoc', 'randomForest',
  'ranger', 'xgboost', 'glmnet'

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

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: 'knitr'

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  'nlstools', 'nls2', 'rmarkdown', 'segmented'

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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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.
Packages required but not available:
  'XML', 'lhs', 'sensitivity', 'dplyr', 'readr', 'purrr', 'furrr',
  'magrittr', 'GenSA', 'genalg', 'raster', 'rstudioapi', 'sf', 'tidyr',
  'tibble', 'crayon', 'igraph', 'stringr', 'progressr', 'EasyABC'

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.
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Package suggested but not available for checking: 'nlstools'

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

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

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.
Package required but not available: 'nlstools'

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

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

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

Packages suggested but not available for checking:
  'minpack.lm', 'optimx', 'Rvmmin', 'Rcgmin', 'numDeriv', 'knitr',
  'rmarkdown', 'Ryacas', 'Deriv'

VignetteBuilder 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:
  'ggplot2', 'minpack.lm', 'nlstools', 'poorman'

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: 'EbayesThresh', 'adlift'

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

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

Packages suggested but not available for checking:
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  'reshape2', 'rmarkdown', 'TESS', 'testthat', 'TreeSim'

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

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

Packages suggested but not available for checking: 'netmeta', 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjags', 'coda', 'ggplot2', 'ks', 'reshape2', 'MCMCpack', 'plotrix',
  'imguR', 'Rdpack'

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:
  'INLA', 'knitr', 'testthat'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/nmaINLA.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/nmaINLA.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:
  'netmeta', 'reshape2', 'ggplot2', 'gridExtra'

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

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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', 'rmarkdown', 'coda'

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.
nnmf_als: no visible global function definition for 'rnorm'
nnmf_mm: no visible global function definition for 'rnorm'
nnmf_prob: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'pkgmaker', 'registry', 'rngtools', 'stringr', 'digest', 'gridBase',
  'colorspace', 'RColorBrewer', 'foreach', 'doParallel', 'ggplot2',
  'reshape2', 'BiocManager', 'Biobase'

Packages suggested but not available for checking:
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  'xtable', 'devtools', 'knitr', 'bibtex', 'RUnit', 'mail'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/NMF-vignette.Rnw'
   'inst/doc/heatmaps.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:
  'dplyr', 'magrittr', 'purrr', 'rappdirs', 'rlang', 'tibble',
  'tidyselect', 'stringr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'systemfit', 'DEoptim', 'data.table', 'magrittr', 'maxLik', 'Rdpack',
  'AER', 'mlogit', 'Hmisc', 'gsubfn', 'abind', 'tidyr', 'plyr', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'recipes', 'Stat2Data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'PMwR', 'RUnit', 'Rglpk', 'datetimeutils', 'quadprog', 'readxl',
  'tinytest'
Packages unavailable to check Rd xrefs: 'PMwR', 'Rglpk', 'quadprog'
Running examples in 'NMOF-Ex.R' failed
The error most likely occurred in:

> ### Name: mvFrontier
> ### Title: Computing Mean-Variance Efficient Portfolios
> ### Aliases: mvFrontier mvPortfolio
> 
> ### ** Examples
> 
> na <- 4
> vols <- c(0.10, 0.15, 0.20,0.22)
> m <- c(0.06, 0.12, 0.09, 0.07)
> const_cor <- function(rho, na) {
+     C <- array(rho, dim = c(na, na))
+     diag(C) <- 1
+     C
+ }
> var <- diag(vols) %*% const_cor(0.5, na) %*% diag(vols)
> 
> wmax <- 1          # maximum holding size
> wmin <- 0.0          # minimum holding size
> rf <- 0.02
> 
> p1 <- mvFrontier(m, var, wmin = wmin, wmax = wmax, n = 50)
Loading required namespace: quadprog
Failed with error:  'there is no package called 'quadprog''
Error in mvFrontier(m, var, wmin = wmin, wmax = wmax, n = 50) : 
  package 'quadprog' is not available
Execution halted
Errors in running code in vignettes:
when running code in 'portfolio.Rnw'
  ...
LIN.DE   0.000208  2.15e-05 1.94e-04 2.66e-04 1.33e-04
MUV2.DE  0.000263  2.84e-05 1.89e-04 1.33e-04 2.59e-04

> minvar(var, wmin = 0, wmax = 0.5)
Loading required namespace: quadprog
Failed with error:  'there is no package called 'quadprog''

  When sourcing 'portfolio.R':
Error: package 'quadprog' is not available
Execution halted

  'An_overview.Rnw'... OK
  'DEnss.Rnw'... OK
  'LSqueens.Rnw'... OK
  'LSselect.Rnw'... OK
  'PSlms.Rnw'... OK
  'TAportfolio.Rnw'... OK
  'portfolio.Rnw'... failed
  'qTableEx.Rnw'... OK
  'repair.Rnw'... OK
  'vectorise.Rnw'... OK
Error(s) in re-building vignettes:
--- re-building 'An_overview.Rnw' using Sweave
found several files...
--- finished re-building 'An_overview.Rnw'

--- re-building 'DEnss.Rnw' using Sweave
Loading required package: NMOF
--- finished re-building 'DEnss.Rnw'

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

--- re-building 'LSselect.Rnw' using Sweave
Loading required package: NMOF
--- finished re-building 'LSselect.Rnw'

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

--- re-building 'TAportfolio.Rnw' using Sweave
Loading required package: NMOF
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'quadprog'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'quadprog'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'quadprog'
--- finished re-building 'TAportfolio.Rnw'

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

Error: processing vignette 'portfolio.Rnw' failed with diagnostics:
 chunk 5 (label = minvar) 
Error in minvar(var, wmin = 0, wmax = 0.5) : 
  package 'quadprog' is not available

--- failed re-building 'portfolio.Rnw'

--- re-building 'qTableEx.Rnw' using Sweave
Loading required package: NMOF
--- finished re-building 'qTableEx.Rnw'

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

--- re-building 'vectorise.Rnw' using Sweave
Loading required package: NMOF
--- finished re-building 'vectorise.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'reticulate', 'R6', 'KernelKnn', 'RcppArmadillo'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'R6', 'pkgload'

Packages suggested but not available for checking: 'brnn', 'validann'

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

Package suggested but not available for checking: 'neuralnet'

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: 'thief'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'nabor', 'units', 'lwgeom', 's2'

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: 'Rcpp'

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 unavailable to check Rd xrefs: 'quadprog', 'bvls'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'doParallel', 'caret', 'data.table', 'dtw', 'dynlm', 'meboot',
  'plyr', 'Rfast', 'rgl', 'stringr', 'tdigest'

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', 'xtable', 'stringr', 'magrittr', 'mvbutils'

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

VignetteBuilder 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', 'rTensor', 'plot3D', 'tagcloud', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survRM2'

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

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown', 'ggplot2', 'ggridges', 'tidyr',
  'forcats', 'mlr', 'mlrCPO'

VignetteBuilder 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', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'dplyr', 'httptest',
  'ggplot2', 'maps', 'mapdata'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'choroplethr', 'choroplethrMaps', 'data.table', 'dplyr', 'forcats',
  'ggplot2', 'hurricaneexposure', 'lubridate', 'maps', 'magrittr',
  'plyr', 'RColorBrewer', 'RCurl', 'rlang', 'stringr', 'tibble',
  'tidyr', 'viridis', 'XML'

Packages suggested but not available for checking:
  'hurricaneexposuredata', 'knitr', 'pander', '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', 'hash', 'digest', 'assertthat', 'purrr', 'dplyr', 'magrittr',
  'crayon', 'rlang', 'stringr'

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', 'rjags', 'coda', 'magrittr'

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

Packages suggested but not available for checking:
  'arrow', 'bit64', 'dplyr', 'dbplyr', 'readr', 'testthat', 'tibble',
  'vroom', 'covr', 'knitr', 'rmarkdown', '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: 'data.table', 'jsonlite'

Packages suggested but not available for checking:
  'sofa', 'elastic', 'mongolite', 'redux', 'RSQLite', 'DBI', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'igraph', 'word2vec', 'rlist', 'dplyr', 'vctrs',
  'vegan'

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

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

Packages suggested but not available for checking:
  'RColorBrewer', 'testthat', 'colorspace'

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', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RWeka', 'kknn', 'caret', 'e1071', 'randomForest', 'rJava'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'magrittr', 'ggplot2', 'preprocessCore',
  'IRanges', 'GenomicRanges', 'Rsamtools', 'philentropy', 'doParallel',
  'foreach'

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: 'gtools', 'ggplot2', '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: 'fracture', 'pkgconfig'

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

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: 'mirt', 'gmodels'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'purrr', 'tidyr', 'magrittr',
  'ggplot2', 'scales', 'treemapify'

VignetteBuilder 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', 'png', 'webshot', 'lifecycle', 'rlang'

Packages suggested but not available for checking:
  'V8', 'knitr', 'rmarkdown', 'testthat', 'shinytest', 'covr',
  'spelling'

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

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

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

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:
  'caret', 'dplyr', 'randomForest', 'ggplot2', 'rlist', 'glmnet',
  'tidyverse', 'e1071', 'purrr', 'pROC', 'rlang'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CondIndTests', 'data.tree', 'caTools', 'randomForest'

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', 'tsDyn', 'minpack.lm'

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

Packages suggested but not available for checking:
  'plot3D', '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:
  'ggplot2', 'gridExtra', 'mvtnorm', 'latticeExtra', 'splines2',
  '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', 'tidyr', 'xml2', 'encode', 'csv', 'spec', 'lazyeval',
  'metaplot', 'magrittr', 'rlang'

Packages suggested but not available for checking:
  'pander', 'knitr', 'wrangle', '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.
Packages required but not available:
  'CompQuadForm', 'mvtnorm', 'lavaan', 'sandwich'

Packages suggested but not available for checking:
  'mirt', 'AER', 'faraway', 'mlogit', 'ordinal', 'pscl', '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: 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'

Package suggested but not available for checking: 'gtools'

Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gtools', 'pracma', 'colorspace', 'doParallel', 'foreach', 'scales'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'sampling', 'e1071', 'glmnet'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'copula'
Note: found 3 marked UTF-8 strings
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'pscl', 'GIGrvg', 'truncnorm', 'pracma', 'HyperbolicDist'

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

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

Package suggested but not available for checking: 'RUnit'

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

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: 'rootSolve'

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

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.
Malformed Description field: should contain one or more complete sentences.
ajb.norm.test: no visible global function definition for 'rnorm'
frosini.norm.test: no visible global function definition for 'var'
frosini.norm.test: no visible global function definition for 'pnorm'
frosini.norm.test: no visible global function definition for 'rnorm'
geary.norm.test: no visible global function definition for 'rnorm'
hegazy1.norm.test: no visible global function definition for 'var'
hegazy1.norm.test: no visible global function definition for 'qnorm'
hegazy1.norm.test: no visible global function definition for 'rnorm'
hegazy2.norm.test: no visible global function definition for 'var'
hegazy2.norm.test: no visible global function definition for 'qnorm'
hegazy2.norm.test: no visible global function definition for 'rnorm'
jb.norm.test: no visible global function definition for 'rnorm'
kurtosis.norm.test: no visible global function definition for 'rnorm'
skewness.norm.test: no visible global function definition for 'rnorm'
spiegelhalter.norm.test: no visible global function definition for
  'rnorm'
wb.norm.test: no visible global function definition for 'qnorm'
wb.norm.test: no visible global function definition for 'var'
wb.norm.test: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for 'cov.wt'
normality.test1: no visible global function definition for 'cor'
normality.test1: no visible global function definition for 'pnorm'
normality.test1: no visible global function definition for 'pchisq'
normality.test2: no visible global function definition for 'cov.wt'
normality.test2: no visible global function definition for 'cor'
normality.test2: no visible global function definition for 'acf'
normality.test2: no visible global function definition for 'pnorm'
normality.test2: no visible global function definition for 'pchisq'
whitenoise.test: no visible global function definition for 'acf'
whitenoise.test: no visible global function definition for 'spec.pgram'
whitenoise.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
Package required but not available: 'astsa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forecast', 'nortest', 'ggplot2', 'gridExtra', 'tseries', 'uroot',
  'zoo'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'igraph', 'tidyverse', 'ggplot2',
  'ggnetwork', 'intergraph', 'viridis', 'gifski', 'png', 'gganimate',
  'ape', 'tidytree', 'treeio', 'ggtree', 'magrittr', '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: 'dplyr', 'gmp'

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

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

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 suggested but not available for checking: 'brms', 'testthat'
Running examples in 'novelforestSG-Ex.R' failed
The error most likely occurred in:

> ### Name: download_model
> ### Title: Download Model Fitted to the 'novelforest' Data
> ### Aliases: download_model
> 
> ### ** Examples
> 
> novelforest_model <- download_model()
To save the model locally, use argument save_to = 'path/filename.rds'
Downloading model (size: 16.5 Mb)
> 
> # library(brms)  # recommended
> summary(novelforest_model)
Loading required package: rstan
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rstan'
Error in .requirePackage(package) : 
  unable to find required package 'rstan'
Calls: summary ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
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:
  'corpcor', 'httr', 'lubridate', 'matlab', 'RCurl', 'xts', 'zoo',
  'DBI', 'magic', 'RMySQL', 'vars'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.newReportId : <anonymous>: 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: 'ggplot2', 'stringr', 'zoo'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Packages required but not available:
  'matrixStats', 'matrixcalc', 'gtools', 'Formula'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'circular', 'misc3d', 'movMF', 'plotrix', 'rgl', 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'copula', 'sandwich'
Package unavailable to check Rd xrefs: 'sandwich'
Packages required but not available: 'permute', 'dplyr', 'coin', 'matlab'

Packages suggested but not available for checking:
  'car', 'mvtnorm', 'plyr', 'xtable'

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

Package suggested but not available for checking: 'KMsurv'

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

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', 'truncnorm', 'ellipse', 'fastcluster', 'ggplot2', 'pheatmap',
  'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'foreach', 'doParallel', 'itertools', 'microbenchmark'

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

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

Packages suggested but not available for checking:
  'knitr', 'shiny', 'shinycssloaders', 'formatR', 'styler', '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: 'ez', 'plyr'

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', '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: 'RUnit', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/nplr.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/nplr.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available:
  'Rmosek', 'R.utils', 'dplyr', 'spatstat', 'latexpdf', 'FDRreg',
  'Rcpp', 'REBayes', 'CAMAN', 'progress', 'pbapply', 'Hmisc', 'pracma',
  'mosaic'

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

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: 'Formula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Packages required but not available:
  'raster', 'ks', 'rgdal', 'lubridate', 'rts', 'snow'

Packages suggested but not available for checking: 'rgeos', 'ncdf4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'anytime', 'futile.logger', 'htmlTable', 'lubridate', 'plotrix',
  'readxl', 'Rlabkey', 'rlang', 'shiny', 'stringi', 'WriteXLS'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'kableExtra', 'knitr', 'markdown',
  'pkgdown', 'png', 'rmarkdown', 'roxygen2', 'shinyBS', 'shinyWidgets',
  '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: 'cubature', 'quadprog', 'quantreg'

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

Package suggested but not available for checking: 'gridExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'e1071', 'randomForest', 'naivebayes', 'ada', 'ROCR',
  'tree'

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'
Package required but not available: '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: 'Formula', 'Rcpp'

Packages suggested but not available for checking: 'snowFT', 'Rmpi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
nps.test: no visible global function definition for 'qnorm'
nps.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Packages required but not available: 'infotheo', 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for 'mclapply'
Undefined global functions or variables:
  mclapply
Package required but not available: 'lsei'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'doParallel', 'matrixcalc', 'StepwiseTest', 'foreach', '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: 'crul', '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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'CCA', 'glmnet', 'PMA', 'roxygen2', 'testthat'
Packages required but not available:
  'httr', 'jsonlite', 'magrittr', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'covr', 'DT', 'httptest', 'shiny', 'shinyBS', 'shinycssloaders',
  'shinythemes', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'coda', 'mcmc', 'mcmcse', 'np', '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', 'roxygen2', 'knitr', 'plyr', 'ggplot2', 'lazyeval',
  'stringr'
Package unavailable to check Rd xrefs: 'lazyeval'
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: 'mco'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'parallelMap', 'rPref', 'xgboost'

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:
  'combinat', 'partitions', 'agricolae', 'ash', 'binom', 'BSDA',
  'coin', 'fANCOVA', 'gtools', 'Hmisc', 'km.ci', 'metafor', 'nortest',
  'np', 'quantreg', 'Rfit', 'SemiPar', 'SuppDists', 'waveslim'

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

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

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

Package suggested but not available for checking: 'mvtnorm'

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

Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'rmarkdown', 'testthat', 'xml2', 'rvest',
  'readr'

VignetteBuilder 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', 'permute', 'ape', 'bigmemory', 'iCAMP'

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 suggested but not available for checking:
  'knitr', 'testthat', 'spelling'
Note: found 1 marked UTF-8 string
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: 'dlm', 'MSwM', 'Rdpack', 'tensor'

Package suggested but not available for checking: 'testthat'

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

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.
Package required but not available: 'snowfall'

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:
  'rlang', 'moments', 'fpc', 'tsibble', 'forecast', 'ggplot2', 'dplyr',
  'purrr', 'tidyr', 'tibble', 'magrittr', 'viridis'

Packages suggested but not available for checking: 'reshape2', '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: 'stringr'

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: 'gmp'
Running examples in 'numbers-Ex.R' failed
The error most likely occurred in:

> ### Name: Bernoulli numbers
> ### Title: Bernoulli Numbers
> ### Aliases: bernoulli_numbers
> 
> ### ** Examples
> 
> bernoulli_numbers(3); bernoulli_numbers(3, big=TRUE)
     [,1] [,2]
[1,]    1    1
[2,]    1    2
[3,]    1    6
[4,]    0    1
Error: Package 'gmp' needed: Please install separately.
Execution halted
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: 'glue'

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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'shiny'

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

VignetteBuilder 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', 'glasso', 'huge', 'tmvtnorm'

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

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

Packages suggested but not available for checking:
  'bookdown', 'covr', 'geosphere', 'knitr', 'png', 'rmarkdown',
  'spelling', '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', 'rsvg', 'grImport2'

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

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

Packages suggested but not available for checking:
  'RColorBrewer', 'qrmdata', 'xts', '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.
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
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.
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for 'flush.console'
nwsPkgInfo: no visible global function definition for
  'packageDescription'
initialize,nwsServer: no visible global function definition for
  'make.socket'
initialize,nwsServer: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'knitr', 'rmarkdown', 'ggplot2',
  'scales', 'ggthemes', 'GGally', 'maps', 'mapproj', 'forcats'

VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 6409 marked UTF-8 strings
Running examples in 'nzelect-Ex.R' failed
The error most likely occurred in:

> ### Name: GE2014
> ### Title: General Election Results 2014
> ### Aliases: GE2014
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # the following matches the results published at
> # http://www.electionresults.govt.nz/electionresults_2014/e9/html/e9_part1.html
> library(tidyr)
Error in library(tidyr) : there is no package called 'tidyr'
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:
  'chron', 'curl', 'httr', 'jsonlite', 'stringr', 'xml2'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 7284 marked UTF-8 strings
Packages required but not available:
  'Rcpp', 'geosphere', 'ggplot2', 'visNetwork', 'data.table',
  'outbreaker2'

Packages suggested but not available for checking:
  'testthat', 'tigris', 'sf', 'knitr', 'socialmixr', '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: 'RColorBrewer'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'httr', 'plyr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'roxygen2', 'DBI', 'knitr', '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: 'oaColors', 'ggplot2'

Package suggested but not available for checking: 'RColorBrewer'

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

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'oaqc_test.R'
Running the tests in 'tests/oaqc_test.R' failed.
Complete output:
  > stopifnot(require('oaqc'), require('igraph'),  getRversion() >= '3.4')
  Loading required package: oaqc
  Loading required package: igraph
  Error: require("igraph") is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'igraph'
  Execution halted
Packages required but not available:
  'rgdal', 'rgeos', 'spdep', 'measurements', 'seg', 'outliers'

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: 'Formula', 'ggplot2', 'reshape2'

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

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.
Packages required but not available:
  'modeest', 'cubature', 'truncdist', 'invgamma', 'LaplacesDemon',
  'HDInterval', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rfast', 'matrixStats', 'stringr', 'readr', 'tibble', 'crayon'

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: 'objectSignals'

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

Package suggested but not available for checking: 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Signal.gen: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'ROCR', 'pls', 'mda', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'pec', 'data.table', 'missForest', 'purrr', 'glmnet',
  'dplyr', 'rlang', 'prodlim', 'ggthemes', 'tidyr', 'ggplot2',
  'scales', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
IBMD: no visible global function definition for 'runif'
IBMD: no visible global function definition for 'quantile'
RAI: no visible global function definition for 'runif'
RAI: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Packages required but not available: 'svDialogs', 'AGread'

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:
  'bazar', 'bit', 'dplyr', 'lazyeval', 'magrittr', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', '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.
obsSensCCC: no visible global function definition for 'coef'
obsSensCCC: no visible global function definition for 'confint'
obsSensCCN: no visible global function definition for 'coef'
obsSensCCN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'coef'
obsSensCNN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'sd'
obsSensCNN: no visible global function definition for 'model.matrix'
obsSensNNN: no visible global function definition for 'coef'
obsSensNNN: no visible global function definition for 'confint'
obsSensNNN: no visible global function definition for 'sd'
obsSensNNN: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
Packages required but not available:
  'bib2df', 'BIEN', 'bit64', 'dplyr', 'ape', 'lubridate', 'rgbif',
  'taxize', 'stringr', 'knitr', 'leaflet', 'htmltools', 'ggplot2',
  'rlang', 'magrittr', 'tidyr', 'RPostgreSQL', 'DBI', 'waffle'

Packages suggested but not available for checking:
  'rmarkdown', 'RColorBrewer', 'viridis', 'remotes', 'RefManageR',
  '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', 'shinyBS', 'shinyjs', 'shinythemes', 'DT', 'sf', 'stringr',
  'leaflet', 'leaflet.extras', 'classInt', 'units', 'ggplot2', 'dplyr',
  'lwgeom', 'mapview'

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

VignetteBuilder 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', 'raster', 'extrafont', 'abind', 'fields',
  'plotrix', 'maptools', 'sp', 'ncdf4', 'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plot3D', 'plot3Drgl', 'rgl', 'shape'

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

Packages suggested but not available for checking:
  'scales', 'oce', '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: 'testthat'

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

Packages suggested but not available for checking:
  'akima', 'automap', 'DBI', 'knitr', 'lubridate', 'marmap', 'ncdf4',
  'ocedata', 'raster', 'rgeos', 'rmarkdown', 'RSQLite', 'R.utils',
  'sp', 'tiff', 'XML'

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

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

Package suggested but not available for checking: 'seriation'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'spam', 'rgl', 'igraph', 'SSN', 'rgdal', 'sp'

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

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: 'pscl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'openssl', 'curl', 'httr', 'jsonlite', '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: 'XML', 'RJSONIO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bit64', 'blob', 'DBI', 'hms', 'rlang', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'DBItest', 'magrittr', 'RSQLite', 'testthat', 'tibble'

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

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
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: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: '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:
  'pcaPP', 'ggplot2', 'ks', 'RcppRoll', 'moments', 'RColorBrewer',
  'mvtsplot', 'tibble', 'reshape', 'dplyr', 'tidyr', 'kernlab',
  'magrittr'

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

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

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

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

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:
  'checkmate', 'deSolve', 'ODEnetwork', 'sensitivity'

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:
  'R6', 'cinterpolate', 'crayon', 'deSolve', 'digest', 'jsonlite',
  'ring'

Packages suggested but not available for checking:
  'dde', 'jsonvalidate', '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: 'gsheet', 'openxlsx'

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

Packages suggested but not available for checking:
  'sf', 'knitr', 'rmarkdown', 'tinytest', 'covr', 'lwgeom'

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 packages required for checking but not installed:
  'rmarkdown', 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'cubature'

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

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', '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:
  'Deriv', 'ggplot2', 'matrixcalc', 'minpack.lm', 'plyr'

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

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:
  'knitr', 'rmarkdown', 'officer', 'xml2', 'rlang', 'uuid', 'yaml',
  'memoise', 'rvg'

Packages suggested but not available for checking:
  'ggplot2', 'flextable', '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: 'R6', 'zip', 'uuid', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'devEMF', 'ggplot2', 'rmarkdown', 'base64enc', 'knitr',
  'rsvg'

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: 'CompQuadForm', 'forestplot'

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

Packages suggested but not available for checking:
  'ade4', 'bnlearn', 'testthat'

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

Packages suggested but not available for checking: 'glmx', 'lmtest'

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

Packages suggested but not available for checking:
  'rlang', 'tidyr', 'forcats', 'microbenchmark', 'testthat',
  'numDeriv', 'ggplot2', 'scales', 'knitr'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'rvest', 'tidyr', 'urltools', 'xml2', 'purrr',
  'rlang'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'lubridate'
Package required but not available: 'plyr'

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

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'

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: 'tkrplot'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'knitr', 'lavaan'
OLScurve: no visible global function definition for 'as.formula'
OLScurve: no visible global function definition for 'na.omit'
OLScurve: no visible global function definition for 'lm'
OLScurve: no visible global function definition for 'predict'
OLScurve: no visible global function definition for 'residuals'
OLScurve: no visible global function definition for 'model.frame'
OLScurve: no visible global function definition for 'model.matrix'
plot.OLScurve : plotOLScurve: no visible global function definition for
  'reshape'
print.OLScurve: no visible global function definition for 'na.omit'
print.OLScurve: no visible global function definition for 'model.frame'
print.OLScurve: no visible global function definition for
  'model.matrix'
print.OLScurve: no visible global function definition for 'cov'
print.OLScurve: no visible global function definition for 'cor'
print.OLScurve: no visible global function definition for 'sd'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'devAskNewPage'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'reshape'
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for 'gray'
subjplot.OLScurve: no visible global function definition for
  'devAskNewPage'
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
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:
  'car', 'data.table', 'ggplot2', 'goftest', 'gridExtra', 'nortest',
  'Rcpp'

Packages suggested but not available for checking:
  'covr', 'descriptr', '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.
fhcor: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Packages required but not available:
  'doParallel', 'ROCR', 'irlba', 'foreach'

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

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

VignetteBuilder 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', 'pheatmap'

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', 'data.table', 'dplyr', 'ff', 'glmnet', 'magrittr',
  'matrixStats', 'purrr', 'rlang', '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.
Packages required but not available: 'psych', 'copula'

Package suggested but not available for checking: 'lavaan'

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

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

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:
  'lazyeval', 'progress', 'rlang', 'data.table', 'Rcpp'

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

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

Packages suggested but not available for checking:
  'testthat', 'magrittr', 'ROI.plugin.glpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gt', 'htmltools', 'magrittr', 'rlang', 'sass', 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'dplyr', 'stringr', 'KEGGREST', 'reshape2', 'ggfortify',
  'ggplot2', 'magrittr', 'tidyr'

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: 'lme4'
Errors in running code in vignettes:
when running code in 'RoeDeerMass-simulation.Rnw'
  ...
> search.range <- c(6, 12)

> search.range.TF <- search.range.CH <- search.range

> res.tf <- onset.test(ll.real, dataFTF, dataMTF, search.range.TF, 
+     do.plot = TRUE)

  When sourcing 'RoeDeerMass-simulation.R':
Error: there is no package called 'lme4'
Execution halted

  'RoeDeerMass-simulation.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'RoeDeerMass-simulation.Rnw' using Sweave

Error: processing vignette 'RoeDeerMass-simulation.Rnw' failed with diagnostics:
 chunk 6 (label = testTF) 
Error in loadNamespace(x) : there is no package called 'lme4'

--- failed re-building 'RoeDeerMass-simulation.Rnw'

SUMMARY: processing the following file failed:
  'RoeDeerMass-simulation.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'assertthat', 'checkmate', 'Formula', 'rstan', 'rstantools',
  'bayesplot', 'ggplot2', 'dplyr', 'tibble', 'tidyr', 'abind',
  'StanHeaders', 'BH', 'RcppEigen'

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

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: 'ade4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
generate.data: no visible global function definition for 'rbinom'
least.common.ancestor: no visible global function definition for
  'na.omit'
oncotree.fit : estimate.error.rates: no visible global function
  definition for 'optim'
plot.boottree: no visible global function definition for 'par'
plot.boottree: no visible global function definition for
  'dev.interactive'
plot.boottree: no visible global function definition for 'mtext'
plot.oncotree: no visible global function definition for 'par'
plot.oncotree: no visible global function definition for 'xinch'
plot.oncotree: no visible global function definition for 'yinch'
plot.oncotree: no visible global function definition for 'lines'
plot.oncotree: no visible global function definition for 'rect'
plot.oncotree: no visible global function definition for 'strwidth'
plot.oncotree: no visible global function definition for 'strheight'
plot.oncotree: no visible global function definition for 'text'
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
Packages required but not available:
  'RCurl', 'jsonlite', 'dplyr', 'xgboost', 'pROC', 'ggplot2', 'caret',
  'DALEX', 'rlist', 'readr', 'rlang', 'formattable', 'sparkline',
  'webshot', 'e1071', 'pdp', 'fs', 'scales', 'tidyr', 'htmltools',
  'rjson'

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:
  'readr', 'magrittr', 'rhdf5', 'data.table', 'Rcpp', 'crayon',
  'dplyr', 'Rhdf5lib'

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: 'Rcpp', 'magrittr'

Packages suggested but not available for checking:
  'genlasso', '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:
  'R6', 'glue', 'safer', 'magrittr', 'jsonlite', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'reshape2', 'Rcpp', 'MDSMap'

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

VignetteBuilder 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', 'dplyr', 'purrr', 'stringr', 'tidyr', 'future',
  'furrr'

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

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: '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', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'fitdistrplus', 'numDeriv'

Package suggested but not available for checking: 'actuar'

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: 'XML', 'RCurl', 'plyr'

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

Packages suggested but not available for checking: 'AID', 'tibble'

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

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: 'VIM'

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', 'R6', 'pbs', 'digest', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp', 'testthat', 'data.table', 'plotly'

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'data.table', 'vroom', 'curl'

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:
  'ontologyIndex', 'paintmap', 'Rgraphviz'

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', 'ontologyIndex'

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

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

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stm', 'purrr', 'tibble', 'shiny', 'miniUI', 'text2vec', 'digest',
  'R6', 'quanteda', 'irr', 'ggplot2', 'cowplot', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'BTM', 'topicmodels', 'keyATM', 'covr', 'stringr',
  'knitr', 'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ci.prop: no visible global function definition for 'qf'
ci.prop: no visible global function definition for 'qnorm'
ePCP: no visible global function definition for 'qnorm'
sevennum: no visible global function definition for 'na.omit'
sevennum: no visible global function definition for 'quantile'
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Packages required but not available:
  'caret', 'dplyr', 'forecast', 'furrr', 'future', 'ggplot2', 'glmnet',
  'imputeTS', 'lmtest', 'lubridate', 'magrittr', 'purrr', 'sandwich',
  'tidyr', 'vars', 'xts', 'zoo'

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

VignetteBuilder 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', 'mime', 'progress'

Packages suggested but not available for checking:
  'e1071', 'knitr', 'knitrBootstrap', '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:
  'rjson', 'RCurl', 'reshape2', 'triangle', 'httpRequest', 'digest',
  'xtable', 'ggplot2', 'rgdal', 'sp', 'plyr', 'igraph'

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'readr', 'dplyr', 'tibble', 'xml2', 'maptools',
  'rappdirs'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'dplyr', 'purrr', 'tidyr', 'readr', 'latticeExtra',
  'lubridate', 'mapproj', 'hexbin', 'Rcpp'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'dplyr', 'lifecycle', 'jsonlite', 'memoise', 'progress',
  'purrr', 'ratelimitr', 'rlang', 'tibble', 'tidyr', 'withr'

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

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.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OpenCL/OpenCL.Rcheck/00install.out' for details.
Packages required but not available:
  'evaluate', 'httpuv', 'knitr', 'jsonlite', 'remotes', 'sys',
  'webutils', 'curl', 'rappdirs', 'zip', 'mime', 'protolite', 'brew',
  'openssl'

Packages suggested but not available for checking:
  'unix', 'haven', 'feather', 'pander', 'R.rsp', 'svglite'

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:
  'secr', 'Rcpp', 'stringr', 'plyr', 'abind', 'RcppParallel'

Packages suggested but not available for checking:
  'knitr', 'RMark', 'rgdal', 'R2ucare', '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', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ckanr', 'magrittr', 'readxl', 'sf', 'tibble', 'xml2', 'curl'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'knitr', 'purrr', '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: 'jsonlite', 'dplyr', 'lubridate'

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:
  'DEoptim', 'dplyr', '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:
  'Rcpp', 'shiny', 'jpeg', 'png', 'tiff', 'R6', 'RcppArmadillo'

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:
  'airports', 'cherryblossom', 'usdata', 'ggplot2', 'readr',
  'rmarkdown', 'tibble'

Packages suggested but not available for checking:
  'broom', 'dplyr', 'forcats', 'knitr', 'lubridate', 'scales', 'tidyr',
  'tidytext'

VignetteBuilder 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', 'ggplot2', 'gridExtra', 'circlize', 'networkD3',
  'raster'

Packages suggested but not available for checking:
  'tmap', 'knitr', 'rmarkdown', 'covr', '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: 'R6'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'BBmisc', 'checkmate', 'data.table', 'digest', 'httr',
  'stringi', 'XML', 'jsonlite', 'memoise', 'curl'

Packages suggested but not available for checking:
  'testthat', 'mlr', 'ParamHelpers', 'randomForest', 'RWeka', 'xml2',
  'farff', 'knitr', 'rmarkdown', 'R.rsp', 'lintr', 'rex'

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:
  'MSEtool', 'DLMtool', 'SAMtool', 'crayon'

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

Packages suggested but not available for checking:
  'mvtnorm', 'numDeriv', 'roxygen2', 'Rmpi', 'rpf', 'snowfall', 'lme4',
  'covr', 'testthat', 'umx', 'ifaTools'

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: 'NLP', 'openNLPdata', 'rJava'

Package suggested but not available for checking: 'openNLPmodels.en'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'shinyBS', 'shinythemes', 'shinyWidgets',
  'shinydashboard', 'shinydashboardPlus', 'shinycssloaders',
  'shinyFeedback', 'rintrojs', 'formattable', 'openxlsx', 'DT',
  'magrittr', 'tidyverse', 'dplyr', 'stringr', 'reshape2', 'scales',
  'igraph', 'testthat', 'tidyr', 'withr', 'RColorBrewer'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'stringr', 'abind', 'rgl', 'colorspace', 'GPArotation',
  'psych', 'XML', 'pvclust', 'openxlsx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'ssh', 'xml2', 'ggmap', 'ggplot2', 'magick', 'R6', 'dbscan'

Packages suggested but not available for checking:
  'knitr', 'BiocStyle', 'RUnit', 'BiocGenerics', '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', 'rlang', 'dplyr', 'osfr', 'hyperSpec', 'hexView',
  'digest', 'signal', 'shiny'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'config', 'shinyjs', 'shinythemes',
  'shinyBS', 'shinyWidgets', 'ggplot2', 'plotly', 'data.table', 'DT',
  'curl', 'rdrop2', 'mongolite', 'loggit'

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: 'askpass'

Packages suggested but not available for checking:
  'testthat', 'digest', 'knitr', 'rmarkdown', 'jsonlite', 'jose',
  'sodium'

VignetteBuilder 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', 'rgrass7', 'progress', 'rgdal', 'sp', 'raster', 'SSN'

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', 'rJava', 'raster', 'rgdal', 'sp'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'maptools', 'openair', 'raster', 'rgdal', 'reshape',
  'doParallel', 'foreach', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'geodist', 'googlePolylines', 'curl',
  'rjson', 'pbapply', 'lubridate', 'sf', 'sfheaders', 'tibble'

Packages suggested but not available for checking:
  'RcppSimdJson', '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:
  'InterVA5', 'InSilicoVA', 'InterVA4', 'Tariff', 'ggplot2', 'crayon',
  'cli'

Packages suggested but not available for checking: 'nbc4va', 'testthat'

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

Packages suggested but not available for checking:
  'knitr', 'testthat', 'roxygen2', '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:
  'quantreg', 'quadprog', 'RColorBrewer', 'testthat', 'caret', 'knitr',
  'gbm', 'htmltools'

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: '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:
  'operators', 'magrittr', '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:
  'ggplot2', 'tibble', 'tidytext', 'magrittr', 'dplyr', 'stringr',
  'purrr', 'tidyr', 'likert', 'cowplot'

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: 'hopbyhop', 'endtoend'
Packages required but not available:
  'magrittr', 'uuid', 'proto', 'cli', 'assertthat', 'tibble', 'ape',
  'tidytree', 'ggplot2', 'viridisLite', 'lpSolveAPI', 'Rcpp',
  'RcppArmadillo', 'RcppProgress'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'roxygen2', 'rmarkdown', 'gurobi', 'ggtree',
  'Rsymphony', 'lpsymphony', 'shiny', 'rhandsontable', '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: 'Rcpp', 'matrixcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nlsolve: no visible global function definition for 'optim'
nlsolve: no visible global function definition for 'runif'
optAUC: no visible global function definition for 'var'
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'LambertW'

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

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: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rpanel', 'randomForest', 'e1071', 'ipred', 'msm', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Ckmeans.1d.dp', 'plotrix', 'Rcpp'

Packages suggested but not available for checking:
  'ape', 'bazar', 'ggplot2', 'knitr', 'reshape2', '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:
  'RankAggreg', 'mclust', 'gplots', 'kohonen', 'MBCluster.Seq'

Packages suggested but not available for checking:
  'Biobase', 'GO.db', 'org.At.tair.db', 'annotate'

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

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.
Malformed Title field: should not end in a period.
Packages required but not available: 'ggplot2', 'magrittr'

Packages suggested but not available for checking:
  'amap', 'dbscan', 'cowplot', 'fastICA', 'fpc', 'ggrepel', 'gtable',
  'knitr', 'plyr', 'reshape2', '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:
  'pbapply', 'pscl', 'betareg', 'ResourceSelection', 'mefa4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringi', '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:
  'lpSolve', 'matrixStats', 'matrixcalc', 'plyr', 'quadprog', 'rgl'

Packages which this enhances but not available for checking:
  'gurobi', 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'momentchi2', 'GreedyExperimentalDesign'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DepthProc', 'fields', 'geometry', 'magrittr', 'mclust', 'nloptr',
  'rsm', 'Rdpack', 'Rdsdp', 'spam', 'stringr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
print.optimbase: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'quantreg', 'mclust', '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: 'lhs', 'randtoolbox', 'stringr'

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', 'colorspace'

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: 'lpSolveAPI', 'tidyr', 'dplyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'R.rsp', 'roxygen2', 'spam', 'microbenchmark', 'testthat', 'ggplot2',
  'numDeriv', 'lbfgsb3c'

VignetteBuilder package required for checking but not installed: 'R.rsp'
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:
  'optextras', 'numDeriv', 'setRNG', 'Rvmmin', 'Rcgmin'

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: 'optimbase'

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

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

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: 'numDeriv'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'setRNG', 'BB', 'ucminf', 'minqa', 'dfoptim',
  'lbfgsb3c', 'lbfgs', 'subplex'

VignetteBuilder 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', 'clinfun'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rootSolve', 'distances', 'weights', 'pbapply', '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.
Package required but not available: '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.
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:
  'data.table', 'ggplot2', 'AUC', 'knitr', 'plyr', 'scales', 'stringr',
  'XML'

Packages suggested but not available for checking:
  '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:
  'plyr', 'kinship2', 'nadiv', 'pedigree', 'pspline', 'stringr',
  'purrr', 'quadprog', 'data.table', 'magic', 'doParallel', 'foreach',
  'ECOSolveR', 'reshape2', 'optiSolve', 'Rcpp', 'RcppArmadillo'

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:
  'shapes', 'alabama', 'cccp', 'nloptr', 'plyr', 'stringr', 'Rcpp'

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

Packages suggested but not available for checking:
  'biglm', 'testthat', 'roxygen2', 'brglm', 'arm', 'knitr',
  'rmarkdown', 'pander', 'xtable'

Packages which this enhances but not available for checking:
  'CBPS', '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: 'SiZer'

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

Packages suggested but not available for checking:
  'covr', 'knitr', '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: 'labdsv', 'plotrix'

Package suggested but not available for checking: 'tree'

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.
Package required but not available: 'igraph'

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

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

Packages suggested but not available for checking: 'cobalt', 'twang'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'VineCopula', 'tea', 'actuar', 'truncnorm', 'ReIns', 'pracma',
  'evmix'

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: 'DBI', 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'graph'
Packages required but not available: 'BiasedUrn', 'BlakerCI', 'PropCIs'

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:
  'raster', 'bookdown', 'knitr', 'latticeExtra', 'plotrix', 'Rcpp',
  'remotes', 'rgdal', 'sf', 'sp'

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.
Package required but not available: 'lmtest'

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

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

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:
  'distances', 'Rfast', 'plyr', 'foreach', 'doRNG', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'splines'
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for 'ecdf'
bgmm : SplineGMM: no visible global function definition for
  'constrOptim'
blr: no visible global function definition for 'ecdf'
blr: no visible global function definition for 'constrOptim'
blr: no visible global function definition for 'lm'
parentcdf : combinations: no visible global function definition for
  'combn'
parentcdf : solver: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package required but not available: 'hash'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'na.tools'
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', 'R6', 'RSQLite', 'digest', 'docopt', 'fs', 'ids', 'withr',
  'yaml', 'zip'

Packages suggested but not available for checking:
  'httr', 'jsonlite', 'knitr', 'mockery', 'processx', 'rmarkdown',
  'testthat', 'vaultr'

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

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

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

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', 'RcppProgress', 'RcppArmadillo', 'BH'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'VGAM'
Packages required but not available: 'reshape2', 'RColorBrewer'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'glmnet', 'penalized', 'VGAM', 'rms'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gtools', 'mvtnorm'

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

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

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: 'mvtnorm', 'corpcor', 'GenOrd'

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

Packages suggested but not available for checking: 'IsoGene', 'Biobase'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'crayon', 'rex', '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
Package required but not available: '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: 'ggplot2', 'ranger', 'Rcpp', '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.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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:
  'ggthemes', 'ggplot2', 'lubridate', 'data.table', 'stringr'

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

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ORICC1: no visible binding for global variable 'sd'
ORICC1: no visible global function definition for 'write.table'
ORICC1: no visible global function definition for 'postscript'
ORICC1: no visible global function definition for 'jpeg'
ORICC1: no visible global function definition for 'points'
ORICC1: no visible global function definition for 'dev.off'
ORICC1: no visible global function definition for 'par'
ORICC2: no visible binding for global variable 'sd'
ORICC2: no visible global function definition for 'write.table'
ORICC2: no visible global function definition for 'postscript'
ORICC2: no visible global function definition for 'jpeg'
ORICC2: no visible global function definition for 'points'
ORICC2: no visible global function definition for 'dev.off'
ORICC2: no visible global function definition for 'par'
Undefined global functions or variables:
  dev.off jpeg par points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages suggested but not available for checking: 'rgl', 'scatterplot3d'
Packages unavailable to check Rd xrefs: 'rgl', 'scatterplot3d'
Running examples in 'orientlib-Ex.R' failed
The error most likely occurred in:

> ### Name: boat3d
> ### Title: Draw boat glyphs for orientation data
> ### Aliases: boat3d
> ### Keywords: hplot dynamic
> 
> ### ** Examples
> 
> x <- eulerzyx(psi=c(0,pi/4,0,0), theta=c(0,0,pi/4,0), phi=c(0,0,0,pi/4))
> 
> # Need a 3D renderer; assume scatterplot3d, but others could be used
> 
> s <- boat3d(x, 0:3, axes = FALSE, graphics = 'scatterplot3d')
Error in boat3d(x, 0:3, axes = FALSE, graphics = "scatterplot3d") : 
  Need 3D renderer:  rgl or scatterplot3d
Execution halted
Packages required but not available:
  'abind', 'data.table', 'assertthat', 'future', 'future.apply',
  'listenv'

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

VignetteBuilder 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', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'TunePareto', 'knitr', 'rmarkdown', 'doParallel', 'igraph',
  'foreach', '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: 'orloca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'png', 'ucminf', '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.
mdr.c: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'rms', 'gtable'

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

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: 'oro.nifti'

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

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

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

Packages which this enhances but not available for checking:
  'fmri', 'oro.dicom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'oro.dicom', 'oro.nifti', 'minpack.lm', 'msm'

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

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

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: 'BB', 'BHH2'

Package suggested but not available for checking: 'setRNG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dr', 'pracma', 'plot3D', 'rgl', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plot.SplineBasis: no visible global function definition for 'matplot'
plot,SplineBasis-matrix: no visible global function definition for
  'matplot'
plot,SplineBasis-missing: no visible global function definition for
  'matplot'
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
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
Package required but not available: 'polynom'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'stringr', 'tm', 'tibble', 'tidytext', 'topicmodels',
  'rmarkdown', 'xlsx', 'knitr'

Packages suggested but not available for checking: 'reshape2', 'qpdf'

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: 'raster'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mc2d'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'optrees', 'optmatch'
Packages unavailable to check Rd xrefs: 'optrees', 'maxmatching', 'optmatch'
Packages required but not available:
  'crul', 'jsonlite', 'stringi', 'purrr', 'tibble', 'rlang', 'fs',
  'memoise', 'httr'

Packages suggested but not available for checking:
  'dplyr', 'logger', 'rprojroot', 'testthat', 'knitr', 'rmarkdown',
  'lintr', 'covr', 'spelling'

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', 'unitizer', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'run.R'
Running the tests in 'tests/run.R' failed.
Complete output:
  > library(unitizer)
  Error in library(unitizer) : there is no package called 'unitizer'
  Execution halted
Packages suggested but not available for checking:
  'askpass', 'testthat', 'withr'
'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: 'XML', 'RCurl', 'geosphere'

Packages suggested but not available for checking: 'igraph', 'sp'

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

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

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', 'geoR', 'mapview', 'nngeo', 'osmdata', 'pdist', 'processx',
  'rgdal', 'sp', 'splancs', 'qpdf', 'Rcpp', 'tibble', 'sf'

Packages suggested but not available for checking:
  'PrevMap', 'rmarkdown', 'markdown', 'leafem', 'viridisLite',
  'raster', '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:
  'rlist', 'knitr', 'rmarkdown', 'stringr', 'ncdf4', 'fields'

VignetteBuilder 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', 'ggm', 'ggplot2', 'mapproj', 'osmdata', 'rgeos', 'sp',
  'spatstat', 'spatstat.core', 'spatstat.geom'

Packages suggested but not available for checking:
  'curl', 'knitr', 'magrittr', '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:
  'OpenStreetMap', 'berryFunctions', 'sp'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: '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', '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:
  'jsonlite', 'curl', 'isoband', 'googlePolylines', 'sp', 'sf'

Packages suggested but not available for checking:
  'mapsf', 'lwgeom', 'tinytest', 'covr'

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

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:
  'Rcpp', 'ggplot2', 'RColorBrewer', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tsne', 'umap', 'HDclust', 'dbscan',
  'flexclust', 'mclust'

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: 'randomForest'

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

Package suggested but not available for checking: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'base64url', 'openssl'

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:
  'checkmate', 'httr', 'geojsonsf', 'janitor', 'jsonlite', 'sf',
  'urltools', 'dplyr', 'rrapply', 'rlang'

Packages suggested but not available for checking: '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:
  'dplyr', 'mice', 'missMDA', 'plyr', 'FactoMineR', 'StatMatch',
  'proxy', 'rdist', 'ROI', 'ROI.plugin.glpk', 'ompr', 'ompr.roi',
  'party', 'vcd'

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: 'mclust', 'foreach', 'doParallel'

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:
  'ggplot2', 'plotly', 'sigmoid', 'reticulate'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'ggplot2', 'gridExtra', 'Hmisc', 'moments', 'quantreg',
  'scales', 'stringi'

Packages suggested but not available for checking:
  'bit64', 'knitr', 'proto', 'testthat'

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

Packages suggested but not available for checking: 'ape', 'geiger'

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

Packages suggested but not available for checking:
  'coda', 'microbenchmark', 'testthat', 'knitr', 'rmarkdown', 'igraph',
  'epicontacts'

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', 'ape', 'incidence'
Running examples in 'outbreaks-Ex.R' failed
The error most likely occurred in:

> ### Name: nipah_malaysia
> ### Title: Nipah in Malaysia and Sinagapore, 1997-1999
> ### Aliases: nipah_malaysia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## show first few weeks of Dengue incidence
> head(nipah_malaysia)
        date perak negeri_sembilan selangor singapore
1 1997-01-04     0               0        0         0
2 1997-01-11     1               0        0         0
3 1997-01-18     0               0        0         0
4 1997-01-25     1               0        0         0
5 1997-02-01     1               0        0         0
6 1997-02-08     0               0        0         0
> 
> ## convert data to incidence object and plot epicurve using the incidence package
> library(incidence)
Error in library(incidence) : there is no package called 'incidence'
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: 'Rdpack'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggplot2', 'knitr', 'testthat', 'tidyr', 'covr',
  'rmarkdown', 'spelling', '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: 'FNN', 'ranger', 'missRanger'

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: 'quantreg', 'Formula'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlist', 'ggplot2', 'dplyr', 'tidyr', 'forcats', 'HDoutliers',
  'robustbase', 'robustX', 'FastPCS', 'cellWise', 'GGally', 'memisc'

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

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:
  'magrittr', 'reshape2', 'sandwich', 'stringr', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'devtools', 'pkgload', 'sys', 'yaml', 'callr', 'tibble',
  'cli'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'outsider.base', 'remotes', 'crayon', 'jsonlite', 'tibble', 'curl',
  'yaml'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'corpcor', 'nloptr', 'geiger', 'RColorBrewer', 'igraph',
  'numDeriv', 'phytools', 'paleotree', 'phangorn', 'lhs', 'interp',
  'phylolm'

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', 'coda', 'Sim.DiffProc', 'MCMCpack', 'abc', 'phytools',
  'TreeSim', 'adephylo', 'maps', 'geiger', 'EasyABC'

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', 'testthat'

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

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

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

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

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

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'pkgdown', 'rmarkdown', 'spelling',
  '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:
  'twang', 'Amelia', 'EnvStats', 'devtools', 'dplyr', 'ggplot2',
  'ggrepel', 'glue', 'magrittr', 'metR', 'purrr', 'progress', 'rlang',
  'survey', 'tibble', 'tidyselect', 'varhandle'

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:
  'tibble', 'dplyr', 'httr', 'jsonlite', 'data.table', 'magrittr'

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

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', 'BH', 'RcppNumerical', 'RcppEigen'

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

VignetteBuilder 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', 'httr', 'jsonlite', 'plyr', 'tibble', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geometa', 'R6', 'httr', 'openssl', 'XML', 'sf', 'rgdal'

Package suggested but not available for checking: 'testthat'

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

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

VignetteBuilder 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', 'jsonlite', 'tibble', 'magrittr', 'tidyr', 'countrycode',
  'stringr'

Packages suggested but not available for checking:
  'curl', 'covr', 'testthat', 'spelling', 'rvest', 'xml2', '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', 'RPostgres', 'dplyr', 'sf', 'dbplyr', 'lubridate',
  'countrycode', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'rvest', 'stringr',
  'RColorBrewer', 'ggplot2', 'DiagrammeR', '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:
  'cli', 'dplyr', 'glue', 'httr', 'jsonlite', 'purrr', 'rjson',
  'rlang', 'stringr', 'tibble', 'tidyr', 'yaml'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
loadCSVtoP2distance: no visible global function definition for
  'read.table'
p2distance : calcularDistancia: no visible binding for global variable
  'sd'
p2distance : ordenarVariables: no visible global function definition
  for 'cor'
p2distance : calculoFactoresPonderacion: no visible global function
  definition for 'lm'
p2distance: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
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.
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'terms'
p3state: no visible global function definition for 'as.formula'
p3state: no visible global function definition for 'coxph'
p3state: no visible binding for global variable 'na.exclude'
plot.p3state: no visible global function definition for 'matplot'
plot.p3state: no visible global function definition for 'devAskNewPage'
plot.p3state: no visible global function definition for 'persp'
plot.p3state: no visible global function definition for 'colours'
plot.p3state: no visible global function definition for
  'filled.contour'
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
pacbpred : thetaFunc: no visible global function definition for 'lsfit'
pacbpred : thetaFunc: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'var'
pacbpred: no visible global function definition for 'runif'
pacbpred: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Packages required but not available: 'diffr', 'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'pander', 'formattable', 'stringr', 'crayon',
  'lubridate', 'tidyr', 'textutils', 'htmlTable', 'clipr', 'shiny',
  'reactable', 'shinyjs', 'shinybusy', 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cranlogs', 'data.table', 'ggplot2', 'memoise', 'pkgsearch', 'RCurl',
  'R.utils', 'rversions', 'sugrrants'

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:
  'callr', 'checkmate', 'crayon', 'cyclocomp', 'desc', 'fakemake',
  'fritools', 'fs', 'gert', 'httr', 'pkgbuild', 'pkgload', 'rcmdcheck',
  'remotes', 'rhub', 'rprojroot', 'whisker', 'whoami'

Packages suggested but not available for checking:
  'cleanr', 'covr', 'devtools', 'digest', 'document', 'knitr', 'lintr',
  'rasciidoc', 'rmarkdown', 'roxygen2', 'RUnit', 'spelling',
  'testthat', 'usethis', 'withr'

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

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

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

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

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 unavailable to check Rd xrefs: 'packS4'
Packages required but not available:
  'readxl', 'stringr', 'data.table', 'reshape2', 'rlang', 'lme4',
  'flexsurv', 'survminer', 'SurvRegCensCov', 'systemfit',
  'IPDFileCheck', 'valueEQ5D', 'car', 'ggplot2', 'lmtest', 'broom',
  'effects', 'gvlma', 'relaimpo', 'tm', 'tidyverse', 'tibble', 'dplyr',
  'tidyr', 'hash', 'haven'

Packages suggested but not available for checking:
  'ISLR', 'knitr', 'rmarkdown', 'covr', '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:
  'fs', 'usethis', 'jsonlite', 'htmlwidgets', 'cli', 'assertthat',
  'rprojroot', 'rstudioapi'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'pROC', 'DiscriMiner', 'doParallel', 'foreach', 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'httr', 'knitr', 'rmarkdown'
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
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
Package unavailable to check Rd xrefs: 'packClassic'
Packages required but not available:
  'penalized', 'lars', 'quadprog', 'limSolve'

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

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

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

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', 'VineCopula', 'numDeriv', 'ggplot2', 'gridExtra',
  'RcppArmadillo'

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', 'igraph', 'parmigene', 'infotheo', 'dplyr', 'Rtsne',
  'ggplot2', 'ggrepel'

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: 'circlize', 'e1071', 'plotrix'

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:
  'RCircos', 'optparse', 'genbankr', 'BiocGenerics', 'Biostrings',
  'GenomicAlignments', 'GenomicRanges', 'IRanges'

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: 'Rcpp', 'dplyr', 'lubridate', 'rlang'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'knitr', 'rmarkdown', 'lazyeval', 'tidyr',
  '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: 'exams', 'stringr', 'curl'

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.
Packages required but not available:
  'Rcpp', 'RColorBrewer', 'VGAM', 'magicaxis', 'networkDynamic',
  'network', 'plyr', 'igraph', 'mapproj', 'knitr'

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.
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'stringr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'ggpubr', '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:
  'igraph', 'ggplot2', 'GGally', 'network', 'sna', 'scales'

Packages suggested but not available for checking:
  'knitr', 'gplots', '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:
  'rmarkdown', 'bookdown', 'htmltools', 'jsonlite', 'later',
  'processx', 'servr', 'httpuv', 'xfun', 'websocket'

Packages suggested but not available for checking:
  'promises', 'testit', 'xaringan', 'pdftools', 'revealjs'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'pagenum-Ex.R' failed
The error most likely occurred in:

> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> 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'
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in ggplot(iris, aes(x = Sepal.Width, y = Sepal.Length, color = Species)) : 
  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 required but not available: 'jsonlite', 'httr', 'curl'

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

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:
  'igraph', 'dendsort', 'drat', 'fastcluster', 'irlba', 'magrittr',
  'N2R', 'plyr', 'R.utils', 'Rcpp', 'rjson', 'rlang', 'R6', 'RMTstat',
  'Rook', 'Rtsne', 'sccore', 'urltools', 'RcppArmadillo',
  'RcppProgress', 'RcppEigen'

Packages suggested but not available for checking:
  'AnnotationDbi', 'base64enc', 'BiocGenerics', 'BiocParallel',
  'colorRamps', 'data.table', 'dbscan', 'dplyr', 'ggplot2', 'GO.db',
  'gridExtra', 'knitr', 'org.Dr.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db',
  'p2data', 'pcaMethods', 'pheatmap', 'rgl', 'rmarkdown', 'robustbase',
  'scde', 'testthat', 'uwot'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'S4Vectors', 'Biostrings', 'ggplot2', 'R6', 'reshape2', 'vegan',
  'GenomicRanges', 'BiocGenerics', 'shinyWidgets', 'shinydashboard',
  'DT', 'plotly', 'magrittr', 'heatmaply', 'dendextend', 'ggfortify',
  'shiny'

Packages suggested but not available for checking:
  'micropan', 'patchwork', 'ape', 'phangorn', 'pegas', 'DECIPHER',
  'rhierbaps', '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: 'lars', 'foreach', 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
paired.Loc: no visible global function definition for 'qt'
paired.Loc: no visible global function definition for 'median'
paired.Loc: no visible global function definition for 'qsignrank'
paired.Loc: no visible global function definition for 'qnorm'
paired.Scale: no visible global function definition for 'var'
paired.Scale: no visible global function definition for 'cor'
paired.Scale: no visible global function definition for 'qt'
paired.Scale: no visible global function definition for 'median'
paired.Scale: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
Packages required but not available: 'gld', 'mvtnorm', 'ggplot2'

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

Package suggested but not available for checking: 'knitr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Sleuth3', 'colorspace', 'multcomp', 'igraph',
  'scales', 'RColorBrewer', 'alr4', 'scagnostics'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BayesFactor', 'dplyr', 'ipmisc', 'parameters', 'PMCMRplus', 'purrr',
  'rlang', 'WRS2'

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

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

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.
Package required but not available: 'data.table'

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.
Package required but not available: 'data.table'

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.
Package required but not available: 'tibble'

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.
Package required but not available: 'tibble'

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.
Package required but not available: 'tibble'

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.
Package required but not available: 'tibble'

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.
Package required but not available: 'tibble'

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.
Package required but not available: 'tibble'

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:
  'assertthat', 'base64enc', 'callr', 'cli', 'cliapp', 'crayon',
  'curl', 'desc', 'filelock', 'glue', 'jsonlite', 'lpSolve',
  'pkgbuild', 'pkgcache', 'prettyunits', 'processx', 'ps', 'R6',
  'rematch2', 'rprojroot', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TeachingDemos', 'rioja', 'tibble', 'dplyr', 'magrittr', 'ggplot2',
  'forcats', 'assertr', 'vegan', 'rlang', 'ggrepel', 'tidyr', 'purrr'

Packages suggested but not available for checking:
  'fields', 'knitr', 'rmarkdown', 'gstat', 'sp', 'tidyverse'

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: 'glmnet'

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

Packages which this enhances but not available for checking:
  'ashr', 'CorShrink', 'pROC', '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:
  'raster', 'maps', 'rjson', 'gtools', 'RCurl', 'plyr', 'scales'

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:
  'GCD', 'locfit', 'raster', 'ggplot2', 'plyr', 'rgdal'

Packages suggested but not available for checking:
  'gtools', 'caTools', 'pscl', 'agricolae', 'Imap', 'sp', 'rworldmap',
  'RColorBrewer'

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 suggested but not available for checking:
  'knitr', 'testthat', 'abind', 'rgl'
Package unavailable to check Rd xrefs: 'rgl'
'LazyData' is specified without a 'data' directory
Running examples in 'paleomorph-Ex.R' failed
The error most likely occurred in:

> ### Name: plotSpecimens
> ### Title: Plot an array of specimen landmark data in an interactive 3D
> ###   frame
> ### Aliases: plotSpecimens
> 
> ### ** Examples
> 
> A <- array(rep(rnorm(3 * 20, sd = 30), by = 6) + rnorm(6 * 20 * 3), 
+        dim = c(20, 3, 6))
> plotSpecimens(A)
Error: Package rgl needed for this function to work. Please install it with install.packages('rgl').
Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'poems', 'R6', 'sf', 'trend'

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

VignetteBuilder 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', 'phytools', 'jsonlite', 'png', 'RCurl'

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:
  'mnormt', 'foreach', 'iterators', 'doParallel'

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:
  'prismatic', 'rematch2', 'rlang', 'rstudioapi'

Packages suggested but not available for checking:
  'covr', 'gameofthrones', 'ggplot2', 'ggthemes', 'harrypotter',
  'knitr', 'oompaBase', 'palr', 'pals', 'rmarkdown', 'scico',
  'testthat', 'vdiffr', 'viridisLite'

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

> ### Name: ichooseyou
> ### Title: Get a pokemon palette. Alias for pokepal.
> ### Aliases: ichooseyou
> 
> ### ** Examples
> 
> library(magrittr)
Error in library(magrittr) : there is no package called 'magrittr'
Execution halted
Package required but not available: 'gsl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tibble', 'ggplot2', 'dplyr', 'tidyr',
  'recipes'
Packages required but not available:
  'Rcpp', 'gsl', 'minqa', 'mvtnorm', '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: 'partykit', 'Formula'

Packages suggested but not available for checking: 'mvtnorm', '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', 'raster', 'testthat', 'covr', 'stars',
  'viridis'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'palr-Ex.R' failed
The error most likely occurred in:

> ### Name: image_pal
> ### Title: Map data values to colours
> ### Aliases: image_pal image_raster image_stars
> 
> ### ** Examples
> 
> set.seed(28)
> vals <- sort(rnorm(100))
> cols <- image_pal(vals, zlim = c(-2.4, 2))
> plot(vals, col = cols); abline(h = 2)
> points(vals, pch  = 19, cex = 0.1) ## zlim excluded some of the range
> if (requireNamespace("raster", quietly = TRUE)) {
+ im <- image_raster(volcano)
+ library(raster)
+ plotRGB(im)
+ }
> if (!requireNamespace("stars", quietly = TRUE)) {
+ library(stars)
+ x <- st_as_stars(volcano)
+ plot(image_stars(x), rgb = 1:3)
+ }
Error in library(stars) : there is no package called 'stars'
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:
  'dichromat', 'colorspace', 'mapproj', 'maps'

Packages suggested but not available for checking:
  'classInt', 'ggplot2', 'knitr', 'latticeExtra', 'reshape2', 'rgl',
  '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: 'mc2d', 'PerMallows', 'Rcpp'

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', '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: 'ade4', 'xtable', 'FactoClass'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Packages required but not available:
  'ggplot2', 'tuneR', 'seewave', 'dplyr', 'magrittr', 'RcppRoll',
  'PamBinaries', 'RSQLite', 'lubridate', 'rerddap', 'ncdf4', 'httr',
  'purrr', 'plotKML', 'hoardr', 'geosphere', 'stringr', 'viridisLite'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'magrittr', 'rlang', 'tidyr', 'ggplot2', 'dplyr',
  'purrr', 'tibble', 'lazyeval', 'Formula', 'mvtnorm', 'pec', 'vctrs'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'PamBinaries', 'dplyr', 'tuneR', 'seewave', 'gam', 'data.table',
  'PAMmisc', 'RSQLite', 'stringr', 'purrr', 'magrittr', 'signal',
  'readr', 'tidyr', 'ggplot2', 'manipulate', 'knitr', 'rstudioapi',
  'xml2', 'rjson', 'rlang', 'reticulate', 'lubridate'

Package suggested but not available for checking: 'testthat'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'Rcpp', 'plotly', 'dplyr', 'curl', 'tidyr',
  'BH', 'RcppEigen', 'RcppParallel', 'StanHeaders'

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

Packages suggested but not available for checking:
  'ggplot2', 'sylly', 'sylly.en', 'futile.logger', 'microbenchmark',
  'zoo', 'descr', 'knitr', 'rmarkdown', 'tables', 'reshape', 'memisc',
  'Epi', 'randomForest', 'tseries', 'gtable', 'rms', 'forecast',
  'data.table'

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: 'jsonlite'

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/pandocfilters.Rnw'
(Is a VignetteBuilder field missing?)

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.
Package required but not available: 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  'model.frame'
Paneldata.formula: no visible global function definition for
  'model.matrix'
Paneldata.formula: no visible global function definition for
  'model.response'
summary.Paneldata: no visible global function definition for 'coef'
summary.Paneldata: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'data.table', 'ggplot2', 'CBPS', 'RcppArmadillo', 'RcppEigen'

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:
  'lme4', 'crayon', 'dplyr', 'Formula', 'ggplot2', 'jtools',
  'lmerTest', 'magrittr', 'purrr', 'rlang', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'car', 'clubSandwich', 'geepack', 'generics',
  'plm', 'sandwich', 'skimr', 'tidyr', '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:
  'knitr', 'progress', 'matrixcalc', 'texreg', 'ggplot2', 'reshape2'

Package suggested but not available for checking: 'rmarkdown'

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: 'data.table', 'Hmisc', 'caret'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'xml2', 'oai', 'tibble', 'hoardr', 'png'

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

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: 'mitools', 'lme4'
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Packages required but not available:
  'neurobase', 'oro.nifti', 'servr', 'htmltools'

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

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

Package which this enhances but not available for checking: 'lme4'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'mlr3misc', 'R6'

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

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

Packages suggested but not available for checking:
  'dtw', 'ggplot2', 'proxy', 'testthat', 'RcppArmadillo',
  'RcppXPtrUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'snowfall', 'raster', 'caret', 'geoR', 'gstat', 'quantregForest',
  'randomForest', 'rgdal', 'sp'

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

Packages suggested but not available for checking:
  'mailR', 'testthat', 'shiny', 'DT', '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: 'BBmisc', 'checkmate'

Packages suggested but not available for checking:
  'BatchJobs', 'batchtools', 'data.table', 'Rmpi', 'snow', 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'bnlearn', 'pcalg', 'Rgraphviz'
Running examples in 'ParallelPC-Ex.R' failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)
Error in library(bnlearn) : there is no package called 'bnlearn'
Execution halted
Package required but not available: 'htmlwidgets'

Packages suggested but not available for checking:
  'testthat', 'shiny', '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', 'foreach', 'doParallel'

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:
  'checkmate', 'data.table', 'set6', '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: 'bayestestR', 'insight'

Packages suggested but not available for checking:
  'AER', 'afex', 'aod', 'BayesFactor', 'BayesFM', 'bbmle', 'betareg',
  'blme', 'brglm2', 'brms', 'broom', 'cAIC4', 'car', 'cgam',
  'clubSandwich', 'cplm', 'dplyr', 'DRR', 'effectsize', 'emmeans',
  'EGAnet', 'FactoMineR', 'fastICA', 'gam', 'gamlss', 'gee', 'geepack',
  'ggplot2', 'GLMMadaptive', 'glmmTMB', 'GPArotation', 'gt', 'lavaan',
  'lavaSearch2', 'lme4', 'lmerTest', 'logspline', 'lqmm', 'knitr',
  'magrittr', 'mclust', 'MCMCglmm', 'mediation', 'metaBMA', 'metafor',
  'mice', 'mfx', 'multcomp', 'multimode', 'MuMIn', 'M3C', 'NbClust',
  'nFactors', 'panelr', 'performance', 'plm', 'PMCMRplus', 'pbkrtest',
  'projpred', 'pscl', 'psych', 'quantreg', 'randomForest', 'rmarkdown',
  'rstanarm', 'sandwich', 'see', 'sjstats', 'spelling', 'survey',
  'testthat', 'TMB', 'tripack', 'truncreg', 'VGAM', 'WRS2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'BBmisc', 'checkmate', 'fastmatch'

Packages suggested but not available for checking:
  'akima', 'covr', 'eaf', 'emoa', 'GGally', 'ggplot2', 'gridExtra',
  'irace', 'lhs', 'plyr', 'reshape2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr', 'lme4', 'survey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'kinship2', 'maxLik'

Packages suggested but not available for checking: 'identity', 'igraph'

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

Packages suggested but not available for checking:
  'openxlsx', 'testthat', 'knitr', 'utf8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'beepr', 'pwr', 'ggplot2', 'knitr', 'lavaan', 'dplyr', 'testthat',
  '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:
  'data.table', 'DiceKriging', 'foreach', 'dbscan', 'lhs', 'crayon',
  'ggplot2', 'ggpubr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xgboost', 'doParallel', '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:
  'mboost', 'party', 'iterators', 'plyr', 'caret', 'glmnet',
  'doParallel'

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

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

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: 'crosstalk', 'htmlwidgets'

Packages suggested but not available for checking:
  'd3r', 'ggplot2', 'htmltools', 'knitr', 'shiny', '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: 'DNAcopy'

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

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', 'lpSolve'

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: 'optimx', 'msm', 'sn'

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', 'SuppDists', 'knitr', 'rmarkdown', 'speedglm',
  'microbenchmark', '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:
  'hansard', 'mnis', 'dplyr', 'stringi', 'sf', 'snakecase', 'readr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'rgdal', 'devtools',
  'leaflet', 'htmltools', 'cartogram', 'htmlwidgets', 'ggplot2',
  'tibble', 'janitor'

VignetteBuilder 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', 'slam', 'Rglpk', 'quadprog', 'corpcor', 'truncnorm'

Packages suggested but not available for checking: 'xts', 'Rsymphony'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rematch2'

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

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

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', 'pbapply', 'snow'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rlang', 'purrr', 'tibble', 'generics', 'glue', 'magrittr',
  'tidyr', 'globals', 'prettyunits', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'keras', 'xgboost', 'covr', 'C50',
  'sparklyr', 'earth', 'kernlab', 'kknn', 'randomForest', 'ranger',
  'modeldata', 'liquidSVM'

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

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

Packages suggested but not available for checking: 'SMNCensReg', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'TH.data', 'VGAM'
Errors in running code in vignettes:
when running code in 'partDSAvig.Rnw'
  ...
Variable importance matrix:
   COG=1 COG=2
x1     0     0
x2     0     2

> data("GBSG2", package = "TH.data")

  When sourcing 'partDSAvig.R':
Error: there is no package called 'TH.data'
Execution halted
when running code in 'survival.Rnw'
  ...
 [6] 0.18696187+ 0.16897759  2.69260249  0.82633336+ 0.02255657 
[11] 1.03854817  2.17975595+ 1.99822549+ 1.27408811  0.24184475+
[16] 0.09781012  0.20884975+ 0.29570876+ 0.57665767  2.46491663+
[21] 0.08316138+ 0.70936374+ 0.06000725+ 0.34905589+ 1.76748093 

> library(VGAM)

  When sourcing 'survival.R':
Error: there is no package called 'VGAM'
Execution halted

  'partDSAvig.Rnw'... failed
  'survival.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'partDSAvig.Rnw' using Sweave
Loading required package: survival

Error: processing vignette 'partDSAvig.Rnw' failed with diagnostics:
 chunk 7 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'TH.data'

--- failed re-building 'partDSAvig.Rnw'

--- re-building 'survival.Rnw' using Sweave

Error: processing vignette 'survival.Rnw' failed with diagnostics:
 chunk 3 
Error in library(VGAM) : there is no package called 'VGAM'

--- failed re-building 'survival.Rnw'

SUMMARY: processing the following files failed:
  'partDSAvig.Rnw' 'survival.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'zoo', 'ggplot2', 'tseries', 'data.table', 'KFAS', 'urca',
  'plot3D'

Packages suggested but not available for checking: 'egcm', 'TTR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partialAR', 'zoo', 'ggplot2', 'TTR', 'data.table', 'glmnet', 'Rcpp',
  'KFAS'

Packages suggested but not available for checking:
  'egcm', '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
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for 'multinom'
fitOR: no visible global function definition for 'formula'
fitOR: no visible global function definition for 'coef'
fitOR: no visible global function definition for 'optim'
reportOR: no visible global function definition for 'qnorm'
reportOR: no visible global function definition for 'pchisq'
reportOR: no visible global function definition for 'coef'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'tidygraph', 'rlang', 'igraph', 'magrittr', 'Rcpp', 'digest', 'dplyr'

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

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: 'Rdpack', 'lpSolve'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'dplyr', 'forcats', 'ggplot2', 'infotheo', 'magrittr',
  'pillar', 'purrr', 'Rcpp', 'rlang', 'stringr', 'tibble', 'tidyr',
  'RcppArmadillo'

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

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

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'pbapply', 'dplyr', 'purrr', 'rlang', 'tibble', 'magrittr',
  'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'future', 'furrr', 'knitr', 'rmarkdown', 'patchwork',
  '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:
  'libcoin', 'mvtnorm', 'Formula', 'inum'

Packages suggested but not available for checking:
  'XML', 'pmml', 'rJava', 'sandwich', 'strucchange', 'vcd', 'AER',
  'mlbench', 'TH.data', 'coin', 'RWeka', 'psychotools', 'psychotree',
  'party', 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'modeltools', 'strucchange', 'coin', 'zoo', 'sandwich'

Packages suggested but not available for checking:
  'TH.data', 'mlbench', 'colorspace', 'vcd', 'ipred', 'varImp',
  'randomForest'

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

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

Packages suggested but not available for checking:
  'testthat', 'randgeo', 'knitr', 'rmarkdown', 'callr', 'pkgbuild',
  'pkgload'

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: 'glmnet'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'VGAM', 'copBasic', 'pcaPP', 'doParallel',
  'foreach', 'tidyverse', 'GGally', 'goftest', 'gridExtra', 'progress',
  'plotly', 'copula', 'Rcpp'

Packages suggested but not available for checking:
  'faraway', 'ordinal', 'rms', 'testthat', 'PResiduals', 'knitr',
  'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'dplyr', 'DT', 'gapminder', 'ggplot2', 'jsonlite', 'knitr',
  'mockr', 'rmarkdown', 'testthat', 'tidyr'

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: 'magrittr', 'dplyr', 'tidyr', 'rlang'

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

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: 'svUnit', 'covr'
Running 'test-with-svUnit.R'
Running the tests in 'tests/test-with-svUnit.R' failed.
Complete output:
  > ## Note that the message in case of error is not explicit enough
  > ## Moreover, nothing is printed in case of success, while we would like a succinct report
  > library(svUnit)
  Error in library(svUnit) : there is no package called 'svUnit'
  Execution halted
Packages required but not available: 'caper', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'e1071'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gtable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gridGraphics', 'gridExtra', 'ragg',
  'testthat', 'vdiffr', 'covr', '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:
  'Rcpp', 'data.table', 'lubridate', 'magrittr', 'dplyr', '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: 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rlang', 'stringi', 'logger'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'config', 'yaml', 'fs', 'magrittr'

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: 'shape'

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/intro-pathdiagram.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'pathfindR'
Note: found 1 marked UTF-8 string
Packages required but not available:
  'pathfindR.data', 'DBI', 'AnnotationDbi', 'doParallel', 'foreach',
  'rmarkdown', 'org.Hs.eg.db', 'ggplot2', 'ggraph', 'ggupset', 'fpc',
  'igraph', 'R.utils', 'magick', 'msigdbr', 'KEGGREST', 'KEGGgraph',
  'knitr'

Packages suggested but not available for checking: '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', 'magrittr', 'glue', 'logging', 'rlang', 'purrr'

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: 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mice', 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BART', 'gbm', 'ggplot2', 'metR', 'pryr', 'twang', 'tidyr'

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:
  'reshape2', 'ggplot2', 'gridExtra', 'plyr', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rlang', 'testthat', 'tibble'

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: 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'landscapemetrics', 'raster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'sp', 'rgdal', 'abind', 'Morpho', 'dplyr', 'imager',
  'magrittr', 'purrr', 'vegan', 'RNiftyReg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'R6', 'ggplot2', 'jpeg', 'png', 'RcppParallel', 'dplyr',
  'gtable', 'gridExtra'

Packages suggested but not available for checking:
  'knitr', 'Cairo', 'RCurl', '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', 'gplots', 'igraph', 'jetset', 'lars', 'limma', 'magic',
  'Mfuzz', 'movMF', 'msgps', 'nnls', 'plotrix', 'SelectBoost', 'tnet',
  'VGAM', 'WGCNA'

Packages suggested but not available for checking:
  'animation', 'Biobase', 'c060', 'elasticnet', 'glmnet', 'pixmap',
  'biomaRt', 'CascadeData', 'repmis', 'knitr', 'R.rsp', 'spls',
  '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', 'equivalence', 'ggplot2', 'lazyeval', 'lubridate',
  'magrittr', 'matchingMarkets', 'reshape2', 'rlang', '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: 'deSolve', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'future.apply', 'geometry', 'lightr', 'magick', 'farver', 'plot3D',
  'progressr', 'sp', 'viridisLite'

Packages suggested but not available for checking:
  'alphashape3d', 'digest', 'imager', 'knitr', 'mapproj', 'rgl',
  '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: 'SparseM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'digest', 'httr', 'ini', 'jsonlite', 'xml2'

Packages suggested but not available for checking:
  'covr', 'rstudioapi', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'paws.compute', 'paws.storage', 'paws.database', 'paws.networking',
  'paws.management', 'paws.machine.learning', 'paws.analytics',
  'paws.security.identity', 'paws.application.integration',
  'paws.cost.management', 'paws.customer.engagement'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rootSolve'

Package suggested but not available for checking: 'kinship2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pbdMPI', 'pbdSLAP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rlecuyer', 'float'

Packages which this enhances but not available for checking:
  'pbdPROF', 'pbdZMQ'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'ade4', 'ape', 'DDD', 'phytools'

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:
  'pbdZMQ', 'remoter', 'pbdMPI'
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/pbdRPC/pbdRPC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rlecuyer', 'pbdMPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'lme4'

Packages suggested but not available for checking: 'ggplot2', 'ca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cmprsk'

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', 'formatR', 'xml2', 'jsonlite', 'zip', 'textclean', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'RCurl', 'ggplot2', 'ggraph',
  'igraph', 'imager', '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:
  'lme4', 'broom', 'dplyr', 'magrittr', 'numDeriv', 'knitr'

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
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'gridExtra'

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: 'metaRNASeq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'PerformanceAnalytics', 'foreach', 'latticeExtra', 'testthat',
  'doParallel', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
'library' or 'require' call to 'foreach' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dotplot.pbo: no visible global function definition for 'reorder'
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
pbo: no visible global function definition for 'lm'
xyplot.pbo: no visible global function definition for 'ecdf'
xyplot.pbo: no visible global function definition for 'doubleYScale'
xyplot.pbo: no visible global function definition for 'reorder'
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
Running 'test_pbo_function.R'
Running the tests in 'tests/test_pbo_function.R' failed.
Complete output:
  > # unit tests for pbo 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(pbo)
  Loading required package: pbo
  Loading required package: lattice
  > 
  > context("Function usage")
  Error in context("Function usage") : could not find function "context"
  Execution halted
a_get_native: no visible global function definition for 'par'
a_get_relative: no visible global function definition for 'par'
brackets: no visible global function definition for 'par'
brackets: no visible global function definition for 'dist'
brackets: no visible global function definition for 'lines'
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: 'PBSmodelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'PBSmodelling'
Packages suggested but not available for checking: 'maptools', 'deldir'
Running examples in 'PBSmapping-Ex.R' failed
The error most likely occurred in:

> ### Name: calcVoronoi
> ### Title: Calculate the Voronoi (Dirichlet) Tesselation for a Set of
> ###   Points
> ### Aliases: calcVoronoi
> ### Keywords: manip
> 
> ### ** Examples
> 
> local(envir=.PBSmapEnv,expr={
+   oldpar = par(no.readonly=TRUE)
+   #--- create some EventData
+   events <- as.EventData(data.frame(
+     EID=1:200, X=rnorm(200), Y=rnorm(200)), projection=1)
+   #--- calculate the Voronoi tesselation
+   polys <- calcVoronoi(events)
+   #--- create PolyData to color it based on area
+   polyData <- calcArea(polys)
+   names(polyData)[is.element(names(polyData), "area")] <- "Z"
+   colSeq <- seq(0.4, 0.95, length=4)
+   polyData <- makeProps(polyData,
+     breaks=quantile(polyData$Z,c(0,.25,.5,.75,1)),
+     propName="col", propVals=rgb(colSeq,colSeq,colSeq))
+   #--- plot the tesselation
+   plotMap(polys, polyProps=polyData)
+   #--- plot the points
+   addPoints(events, pch=19)
+   par(oldpar)
+ })
Loading required package: deldir
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'deldir'
Error in .checkRDeps("calcVoronoi", c("deldir")) : 
The function 'calcVoronoi' requires the package(s) 'deldir'.
Please install the package(s) and try again.
Calls: local ... eval -> eval -> eval -> eval -> calcVoronoi -> .checkRDeps
Execution halted
Package required but not available: 'XML'

Packages suggested but not available for checking: 'PBSmapping', 'deSolve'

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', 'RcppArmadillo'

Package suggested but not available for checking: 'pbivnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'ellipse'

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: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mixOmics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FactoMineR', 'RColorBrewer'

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:
  'bigutilsr', 'data.table', 'ggplot2', 'magrittr', 'mmapcharr',
  'Rcpp', 'RSpectra', 'rmio'

Packages suggested but not available for checking:
  'plotly', 'shiny', 'spelling', 'testthat', 'vcfR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'reshape2', 'pander', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'graph', 'RBGL', 'igraph', 'ggm', 'corpcor', 'robustbase',
  'vcd', 'Rcpp', 'bdsmatrix', 'sfsmisc', 'fastICA', 'clue',
  'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'Rgraphviz', 'mvtnorm', 'huge', 'ggplot2', 'dagitty'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exact2x2', 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rdpack'

Packages suggested but not available for checking:
  'covr', '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:
  'optmatch', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'PCAmatchR-Ex.R' failed
The error most likely occurred in:

> ### Name: match_maker
> ### Title: Weighted matching of controls to cases using PCA results.
> ### Aliases: match_maker
> 
> ### ** Examples
> 
> # Create PC data frame by subsetting provided example dataset
> pcs <- as.data.frame(PCs_1000G[,c(1,5:24)])
> # Create eigenvalues vector using example dataset
> eigen_vals <- c(eigenvalues_1000G)$eigen_values
> # Create full eigenvalues vector using example dataset
> all_eigen_vals<- c(eigenvalues_all_1000G)$eigen_values
> # Create Covarite data frame
> cov_data <- PCs_1000G[,c(1:4)]
> # Generate a case status variable using ESN 1000 Genome population
> cov_data$case <- ifelse(cov_data$pop=="ESN", c(1), c(0))
> # With 1 to 1 matching
>  if(!requireNamespace("optmatch", quietly = TRUE)){
+                         match_maker(PC = pcs,
+                                     eigen_value = eigen_vals,
+                                     data = cov_data,
+                                     ids = c("sample"),
+                                     case_control = c("case"),
+                                     num_controls = 1,
+                                     eigen_sum = sum(all_eigen_vals),
+                                     weight_dist=TRUE
+                                    )
+                           }
Error in match_maker(PC = pcs, eigen_value = eigen_vals, data = cov_data,  : 
  The package optmatch (>= 0.9-1) not loaded.  To run the PCAmatchR match_maker()
          function, you must manually install and load the "optmatch" package first and
          agree to the terms of its license.  This is required due to software license
          issues.
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
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: 'mvtnorm'

Package suggested but not available for checking: 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat', 'readr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ClassDiscovery', 'oompaBase', 'kernlab', 'changepoint', 'cpm'

Package suggested but not available for checking: 'nFactors'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'freqdom', 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nleqslv', 'matrixcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RMTstat', 'corpcor'

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/pcev.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'reshape2', 'mvtnorm', 'igraph', 'loo', 'lifecycle',
  'RcppEigen', 'StanHeaders', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'shiny', 'ggplot2', 'covr',
  'qgraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pcalg', 'graph', 'Hmisc', 'lme4', 'sommer', 'ggm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'safe', 'RMTstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigmemory', 'bigstatsr', 'bnlearn', 'Rfast', 'Rfast2', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RUnit'
Running 'bootstrap.R'
  Running 'test_functions.R'
Running the tests in 'tests/test_functions.R' failed.
Complete output:
  > library(PCICt)
  > library(RUnit)
  Error in library(RUnit) : there is no package called 'RUnit'
  Execution halted
Packages required but not available: 'Rcpp', 'combinat'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'svd'

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:
  'ape', 'distory', 'geiger', 'mvSLOUCH', 'phangorn', 'TreeSim',
  'yuima'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'PCMBase', 'data.table', 'abind', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

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:
  'ape', 'expm', 'mvtnorm', 'data.table', 'ggplot2', 'xtable'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'abind', 'ggtree', 'cowplot',
  'covr', 'mvSLOUCH', 'BiocManager'

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:
  'ltm', 'statmod', 'cubature', 'mvtnorm', 'Rcpp', '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: 'fda', 'pracma', 'deSolve'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Hmisc', '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: 'GPArotation', 'ThreeWay'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'ggplot2', 'prodlim',
  'riskRegression', 'PermAlgo', 'pec', '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:
  'SYNCSA', 'ape', 'picante', 'phylobase', 'vegan', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bcp', 'changepoint', 'chipPCR', 'ecp', 'fda.usc', 'MBmca',
  'pbapply', 'pracma', 'qpcR', 'robustbase', 'segmented', 'shiny',
  'zoo'

Packages suggested but not available for checking:
  'DT', 'future', 'knitr', 'listenv', 'RDML', 'readxl', 'rmarkdown',
  'shinycssloaders', 'spelling', 'testthat', 'xtable'

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'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'cowplot'

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: 'statmod', 'multtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'Rdpack'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'spelling'

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'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stplanr', 'readr', 'sf'

Packages suggested but not available for checking:
  'covr', 'curl', 'dplyr', 'ggplot2', 'knitr', 'leaflet', 'pbapply',
  'remotes', 'rmarkdown', 'testthat', 'tmap'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sarima', 'BB', 'PolynomF', 'gbutils', 'zoo', 'xts', 'lagged',
  'mcompanion', 'Rdpack', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'fUnitRoots', 'partsm', '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', 'httr', 'rvest', 'jsonlite', 'data.table', 'RcppArmadillo'

Package suggested but not available for checking: 'imager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotrix'
Package required but not available: 'tcltk2'

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:
  'car', 'dplyr', 'ggplot2', 'lmtest', 'msm', 'pglm', 'plm', 'splm',
  'texreg'
Running examples in 'pder-Ex.R' failed
The error most likely occurred in:

> ### Name: DemocracyIncome
> ### Title: The Relation Between Democraty and Income
> ### Aliases: DemocracyIncome
> ### Keywords: datasets
> 
> ### ** Examples
> 
> #### Example 7-1
> 
> ## ------------------------------------------------------------------------
> 
> data("DemocracyIncome", package = "pder")
> 
> ## ------------------------------------------------------------------------
> data("DemocracyIncome", package="pder")
> set.seed(1)
> di2000 <- subset(DemocracyIncome, year == 2000,
+                  select = c("democracy", "income", "country"))
> di2000 <- na.omit(di2000)
> di2000$country <- as.character(di2000$country)
> di2000$country[- c(2,5, 23, 16, 17, 22, 71,  125, 37, 43, 44,
+                    79, 98, 105, 50, 120,  81, 129, 57, 58,99)] <- NA
> 
> library("ggplot2")
Error in library("ggplot2") : there is no package called 'ggplot2'
Execution halted
Package required but not available: 'geometry'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'zoo', 'xts', 'XML', 'lubridate', 'jsonlite', 'reshape2',
  'readr', 'curl', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'checkmate', 'jsonlite'

Packages suggested but not available for checking: 'PythonInR', 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pdftools', 'tibble', 'tokenizers', 'stringi'

Packages suggested but not available for checking:
  'shiny', '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: '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: 'Rcpp', 'qpdf'

Packages suggested but not available for checking:
  'jpeg', 'png', 'webp', 'tesseract', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'purrr', 'randomForest', 'readxl', 'stringr',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'ggplot2'

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.
pdist: no visible global function definition for 'dist'
pdist: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'mco'

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'ggplot2', 'network'

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', 'dendextend', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridExtra', 'magrittr', 'plyr', 'viridis'

Packages suggested but not available for checking:
  'adabag', 'AmesHousing', 'C50', 'caret', 'Cubist', 'doParallel',
  'dplyr', 'e1071', 'earth', 'gbm', 'ipred', 'keras', 'kernlab', 'mda',
  'party', 'partykit', 'progress', 'randomForest', 'ranger',
  'testthat', 'xgboost', 'knitr', 'rmarkdown', 'vip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'knitr', 'pillar', 'rmarkdown', 'spelling', 'testthat',
  'vdiffr'

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: 'orthopolynom', 'moments'

Packages suggested but not available for checking:
  'ggplot2', 'reshape2', 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/PDQutils.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plm', 'car', 'coefplot', 'lmtest', 'sandwich', 'papeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rly'

Packages suggested but not available for checking:
  'testthat', 'covr', 'lintr', 'knitr', 'curl', '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.
band.chol.cv: no visible global function definition for 'cov'
pdsoft.cv: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Package required but not available: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'multitaper', 'Rcpp', 'ddalpha', 'Rdpack', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'reshape2', 'viridis',
  'ggthemes'

VignetteBuilder 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', 'rlang', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet', 'leaflet.extras', 'gganimate',
  'infer', 'moderndive', 'readr', 'gifski', 'ggplot2', 'forcats'

VignetteBuilder 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', 'optimx', 'qlcMatrix', 'Rdpack'

Packages suggested but not available for checking:
  'plm', 'pder', '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:
  'lubridate', 'magrittr', 'dplyr', 'geosphere', 'tidyr', 'stringr',
  'rlang'

Packages suggested but not available for checking:
  'countrycode', 'tibble', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mnormt', 'metap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running examples in 'PeakError-Ex.R' failed
The error most likely occurred in:

> ### Name: PeakError
> ### Title: PeakError
> ### Aliases: PeakError
> 
> ### ** Examples
> 
> x <- seq(5, 85, by=5)
> peaks <- rbind(Peaks("chr2", x, x+3),
+                Peaks("chr3", c(25, 38, 57), c(33, 54, 75)),
+                Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)),
+                Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85)))
> regions <- NULL
> for(chr in 1:5){
+   regions <- rbind(regions, {
+     data.frame(chrom=paste0("chr", chr),
+                chromStart=c(10, 30, 50, 70),
+                chromEnd=c(20, 40, 60, 80),
+                annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
+   })
+ }
> err <- PeakError(peaks, regions)
> ann.colors <-
+   c(noPeaks="#f6f4bf",
+     peakStart="#ffafaf",
+     peakEnd="#ff4c4c",
+     peaks="#a445ee")
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running 'script.R'
Running the tests in 'tests/script.R' failed.
Last 13 lines of output:
  > overlapping.bed <- file.path(exampleData, "overlapping_peaks.bed")
  > 
  > ##test_that("PeakError_compute.R correct", {
  > out.file <- tempfile()
  > cmd <- paste(Rscript, PeakError_compute.R, peaks.bed, labels.bed, ">", out.file)
  > status <- system(cmd)
  Error: Usage: compute_error.R peaks.bed labels.bed > errors.bed
  Execution halted
  > errors <- read.table(out.file, sep="\t", header=TRUE)
  Error in file(file, "rt") : cannot open the connection
  Calls: read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\PeakError\tmp\RtmpI3NhLD\filef588ce042f1': No such file or directory
  Execution halted
Package required but not available: '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.
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: 'data.table'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'future.apply', 'future', 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Examples.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'penaltyLearning'
Running examples in 'PeakSegDP-Ex.R' failed
The error most likely occurred in:

> ### Name: chr11ChIPseq
> ### Title: ChIP-seq aligned read coverage for 4 samples on a subset of
> ###   chr11
> ### Aliases: chr11ChIPseq
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chr11ChIPseq)
> 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: 'PeakError', 'penaltyLearning'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'microbenchmark'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'penaltyLearning'

Packages suggested but not available for checking:
  'PeakSegDP', 'ggplot2', 'testthat', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gsl'
Package unavailable to check Rd xrefs: 'gsl'
PearsonICA: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'dev.new'
PearsonICAdemo: no visible global function definition for 'par'
PearsonICAdemo: no visible global function definition for 'axis'
PearsonICAdemo: no visible global function definition for 'title'
PearsonICAdemo: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis dev.new lines par rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'prodlim', 'foreach', 'rms', 'riskRegression', 'lava', 'timereg'

Packages suggested but not available for checking:
  'randomForestSRC', 'party', 'cmprsk', 'crrstep', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pedtools', 'pedprobr', 'forrel', 'glue'

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', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompQuadForm', 'survey', 'kinship2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'HaploSim', 'reshape'

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'
'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: 'latticeExtra', 'Rcpp'

Packages suggested but not available for checking:
  'car', 'fields', 'geoR', 'georob', 'gstat', 'knitr', 'moments',
  'pbapply', 'plyr', 'randomForest', 'RColorBrewer', 'sp',
  'SpatialTools', 'spsurvey', 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pedtools', 'pedmut'

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', 'TTR', 'zoo', 'curl', 'xml2', 'httr', 'rvest',
  'jsonlite', 'stringi', 'readxl', 'readr', 'ggplot2', 'scales',
  'gridExtra', 'plotly'

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
Package required but not available: 'kinship2'

Packages suggested but not available for checking:
  'testthat', 'igraph', 'knitr', 'rmarkdown', 'pedmut', '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: 'sandwich', 'lmtest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'adegenet'

Packages suggested but not available for checking: 'rgl', 'snpStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bvls', 'RSEIS', 'pracma', 'geigen', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DT', 'shiny'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
PEMM_fun : find.lambda: no visible global function definition for
  'optimize'
PEMM_fun: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Packages required but not available:
  'loa', 'RColorBrewer', 'latticeExtra', 'baseline', 'ggplot2',
  'rlang', 'dplyr', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'penalized', 'clogitL1', 'tidyverse'

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: 'flsa'

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: 'globaltest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'mlegp', 'corpcor', 'statmod', 'tgp', 'lhs'

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:
  'neuroblastoma', 'jointseg', 'testthat', 'future', 'future.apply',
  'directlabels'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'doParallel', 'glmnet', 'survcomp', 'survivalROC',
  'dplyr', 'magic', 'lcmm'

Packages suggested but not available for checking:
  'ptmixed', 'survminer', '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:
  'fda', 'latticeExtra', 'pacotest', 'quadprog', 'doParallel',
  'foreach', 'TSP', 'igraph'

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: 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TSP', 'fda', 'foreach', 'quadprog', 'latticeExtra', 'doParallel'

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.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'Rdpack', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'lifecycle', 'rlang', '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.
Package required but not available: 'penalized'

Packages suggested but not available for checking: 'survivalROC', '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: 'snowfall'

Packages suggested but not available for checking: 'locfit', 'penalized'

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:
  'yaml', 'stringr', 'pryr', 'data.table'

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: 'elasticnet'

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/Paper_Analysis.Rnw'
   'inst/doc/PepSAVIms_Introduction.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'discreteRV', 'plyr', 'dplyr'

Package suggested but not available for checking: 'ggplot2'

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', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'corpcor', 'gnm', 'matlab', 'signal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'multcomp'

Packages suggested but not available for checking:
  'magrittr', 'spelling', 'dplyr', 'knitr', 'rmarkdown', 'testthat',
  'ggplot2', 'carData', 'tidyr', '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', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'assertive.types', 'assertthat', 'R6'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'devtools', 'reshape2'

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:
  'ape', 'phytools', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'HHG', 'dendextend', 'vcfR', '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:
  'ltm', 'mirt', 'fda', 'Hmisc', 'irtoys'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'limma', 'graph', 'RBGL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'quadprog', 'zoo'

Packages suggested but not available for checking:
  'dygraphs', 'Hmisc', 'quantmod', 'gamlss', 'gamlss.dist',
  'robustbase', 'quantreg', 'tinytest', 'ggplot2', 'RColorBrewer',
  'googleVis', 'plotly', 'gridExtra', 'ggpubr', 'RPESE', 'R.rsp',
  'RobStatTM'

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:
  'ggplot2', 'parallelMap', 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'e1071', 'DMwR', 'randomForest',
  'quantmod', 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bayestestR', 'insight'

Packages suggested but not available for checking:
  'AER', 'BayesFactor', 'betareg', 'bigutilsr', 'brms', 'car',
  'CompQuadForm', 'correlation', 'cplm', 'dbscan', 'fixest',
  'forecast', 'gamm4', 'ggplot2', 'glmmTMB', 'gridExtra', 'ICS',
  'ICSOutlier', 'ISLR', 'lavaan', 'lme4', 'lmtest', 'loo', 'magrittr',
  'metafor', 'mlogit', 'nonnest2', 'ordinal', 'parameters', 'pscl',
  'psych', 'randomForest', 'rmarkdown', 'rstanarm', 'rstantools',
  'sandwich', 'see', 'spelling', 'survey', 'testthat', 'tweedie',
  'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'seriation'

Packages suggested but not available for checking:
  'knitr', 'gclus', 'dendextend', 'dendextendRcpp', '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: 'Hmisc', 'rms'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyBS', 'lubridate', 'DT', 'writexl',
  'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shinydashboardPlus', 'testthat',
  'canvasXpress', 'openxlsx'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
permalgorithm: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xtable', 'scales', 'deldir'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'Biobase'
Package required but not available: 'coin'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ipred', 'party', 'randomForest'

Packages suggested but not available for checking:
  'knitr', '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: '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/permPATHmanual.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'coin'
Malformed Description field: should contain one or more complete sentences.
ksample.pclt: no visible global function definition for 'pchisq'
pCI: no visible global function definition for 'qbeta'
permKS.formula: no visible global function definition for 'terms'
permTREND.default: no visible global function definition for 'cor'
permTREND.formula: no visible global function definition for 'terms'
permTS.formula: no visible global function definition for 'terms'
trend.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Running 'perm.coin.check.R'
Running the tests in 'tests/perm.coin.check.R' failed.
Complete output:
  > ## check perm against coin (ver 1.0-8 or greater)
  > library(perm)
  > library(coin)
  Error in library(coin) : there is no package called 'coin'
  Execution halted
Packages required but not available:
  'ggplot2', 'rlang', 'dabestr', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'permute'

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: 'magic', 'numbers', 'partitions'

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 suggested but not available for checking: 'vegan', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## Test `permute` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: 'plyr'

Packages suggested but not available for checking:
  'buildmer', 'car', 'doParallel', 'dplyr', 'ggplot2', 'lmPerm',
  'lme4', 'permuco', 'pbkrtest', 'tidyr', 'knitr', '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: 'ggplot2', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'XML', 'Biobase', 'stringr'

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.
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Packages required but not available: 'jpeg', 'tiff', 'stringr', 'raster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'personalized', 'HDtweedie', 'Rcpp', 'foreach', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'gbm', 'ggplot2', 'plotly', 'kernlab', 'foreach'

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:
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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.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'rlang', 'rlist', 'stringr', 'tibble'

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: 'igraph', '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: 'magrittr', 'rlang'

Packages suggested but not available for checking: 'testthat', 'purrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readxl', 'stringr'

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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  'rlang', 'RSQLite', 'tidyr'

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:
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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.
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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:
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  'FD', 'animation', 'phytools'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/pez-intro.Rnw'
   'inst/doc/pez-pglmm-overview.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lars', 'POET', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'corpcor', 'moments'

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:
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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.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maxLik', 'plm', 'statmod', 'Formula'

Packages suggested but not available for checking: 'lmtest', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'JGL', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'randtoolbox', 'pracma', 'RcppArmadillo'

Packages suggested but not available for checking: 'anMC', 'DiceDesign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SAM', 'energy', 'glasso', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'gridExtra'

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  'knitr', 'rmarkdown', 'pander'

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.
Package required but not available: 'Rcpp'

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: 'gsDesign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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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.
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'readxl', 'kableExtra', 'plyr', '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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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', 'mvtnorm', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'ggplot2', 'rjags', 'arrayhelpers', 'reshape2', 'plyr',
  'dplyr', 'RColorBrewer', 'gridExtra', 'kableExtra', '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: 'BiocParallel'

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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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: 'RColorBrewer', 'scales', 'gtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'RMySQL'

Packages suggested but not available for checking:
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  '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:
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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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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: 'ppcor', 'SuppDists'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'reshape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gstat', 'RColorBrewer', 'pheno'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'changepoint', 'httr', 'zoo', 'memoise', 'daymetr',
  'MODISTools'

Packages suggested but not available for checking:
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  'leaflet', 'plotly', 'DT'

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: 'rjags'

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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  'lubridate', 'data.table', 'spam', 'gridExtra', 'magrittr', 'plyr',
  'reshape2', 'zoo', 'optimx', 'ucminf', 'numDeriv', 'shiny',
  'jsonlite', 'foreach', 'iterators', 'JuliaCall', 'RcppArmadillo'

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:
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Packages suggested but not available for checking:
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  'pbapply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'phenex', 'plyr', 'raster', 'stringr', 'rgdal', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'plyr', 'jpeg', 'stringr', 'bcp', 'strucchange', 'foreach',
  'doParallel', 'iterators', 'gtools', 'raster', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SparseM', 'quantreg'

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'
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: 'lme4', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'optparse', 'R.utils', 'mvtnorm', 'snpStats', 'zoo', 'data.table',
  'Rcpp', 'cowplot', 'ggplot2', 'reshape2', 'dplyr'

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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  'randomForest', 'Rcpp', 'tidyr', 'viridis', 'zoo'

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: 'car'

Package suggested but not available for checking: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', '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.
Packages required but not available: 'data.table', 'janitor'

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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Package suggested but not available for checking: 'KMsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'slam', 'tm', 'shiny'

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:
  'tuneR', 'phonTools', 'rmarkdown', 'xml2', 'uchardet'

Packages suggested but not available for checking:
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  'testthat', 'readxl'

VignetteBuilder 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', '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: 'splancs', 'deldir', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'photobiology'

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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  'readr', 'readxl', 'lazyeval', 'colorSpec'

Packages suggested but not available for checking:
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  'photobiologyWavebands', '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: 'photobiology'

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: 'photobiology'

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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  'tidyr', 'splus2R', 'zoo', 'rlang'

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: 'photobiology'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'photobiologyWavebands', 'ggspectra', '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: 'photobiology'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'photobiologyWavebands', 'ggplot2',
  'ggspectra', 'lubridate'

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: 'photobiology'

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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  'furrr', 'future', 'glue', 'gunit', 'magrittr', 'pkgnet', 'purrr',
  'rlang', 'stringr', 'tealeaves', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', '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: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'LBE', 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridExtra', 'manipulate', 'testthat'

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: 'phylobase', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'geometry', 'raster', 'gdistance'
Running examples in 'phylin-Ex.R' failed
The error most likely occurred in:

> ### Name: extract.val
> ### Title: Extact pairwise values from a matrix in a specified order.
> ### Aliases: extract.val
> ### Keywords: variogram kriging
> 
> ### ** Examples
> 
> 
> data(vipers)
> data(d.gen)
> 
> # calculate midpoints
> mp <- midpoints(vipers[,1:2])
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.
Execution halted
Errors in running code in vignettes:
when running code in 'phylin_tutorial.Snw'
  ...
> grid.image(krg, grid, main = "Potential contact zones / single threshold", 
+     xlab = "Longitude", ylab = "Latitude", sclab = "Prob. of multiple  ..." ... [TRUNCATED] 

> points(vipers[, 1:2], cex = 0.5)

> mp <- midpoints(vipers[, 1:2])

  When sourcing 'phylin_tutorial.R':
Error: Package 'geometry' is needed for Delaunay triangulation.
Execution halted
when running code in 'resistance_tutorial.Snw'
  ...
+     5)))

> plot(simul.env$env.sur, conductance, cex = 0.25, xlab = "Environmental surface", 
+     ylab = "Conductance")

> library(gdistance)

  When sourcing 'resistance_tutorial.R':
Error: there is no package called 'gdistance'
Execution halted

  'phylin_tutorial.Snw' using 'UTF-8'... failed
  'resistance_tutorial.Snw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'phylin_tutorial.Snw' using Sweave

Error: processing vignette 'phylin_tutorial.Snw' failed with diagnostics:
 chunk 31 (label = midpoints) 
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.

--- failed re-building 'phylin_tutorial.Snw'

--- re-building 'resistance_tutorial.Snw' using Sweave

Error: processing vignette 'resistance_tutorial.Snw' failed with diagnostics:
 chunk 7 (label = conductanceraster) 
Error in library(gdistance) : there is no package called 'gdistance'

--- failed re-building 'resistance_tutorial.Snw'

SUMMARY: processing the following files failed:
  'phylin_tutorial.Snw' 'resistance_tutorial.Snw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ade4', 'ape', 'Rcpp', 'rncl', 'RNeXML'

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/phylobase.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'phylobase', 'htmlwidgets'

Packages suggested but not available for checking:
  'magrittr', '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', 'raster', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'sys'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ape'

VignetteBuilder 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', 'capushe', 'foreach', 'gglasso', 'glmnet', 'LINselect',
  'plyr', 'Rcpp', 'robustbase', 'RcppArmadillo'

Packages suggested but not available for checking:
  'combinat', 'doParallel', 'phytools', 'testthat', 'TreeSim', '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'

Packages suggested but not available for checking:
  'dendextend', '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: 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'future.apply'

Package suggested but not available for checking: 'testthat'

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.
Package required but not available: '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:
  'ape', 'ggm', 'ggplot2', 'ggraph', 'igraph', 'MuMIn', 'pbapply',
  'phylolm', 'purrr', 'tibble'

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:
  'ape', 'phangorn', 'betapart', 'raster', 'colorspace', 'vegan', 'sp',
  'igraph', 'rgdal', 'rgeos'

Packages suggested but not available for checking:
  'tinytest', 'knitr', 'rmarkdown', 'mapproj'

VignetteBuilder 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', 'phyloseq', 'ggnetwork', 'igraph', '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.
Packages required but not available:
  'Rcpp', 'adephylo', 'igraph', 'ape', 'phylobase', 'DBI',
  '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.
Package suggested but not available for checking: 'ape'
Package required but not available: 'ape'

Package suggested but not available for checking: 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'igraph', 'NHPoisson', 'phylobase'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'Rcpp', 'dplyr', 'lme4', 'nloptr', 'gridExtra', 'mvtnorm',
  'latticeExtra', 'tidyr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'pez', 'knitr', 'rmarkdown', 'covr', 'picante',
  'rbenchmark', 'INLA', 'MCMCglmm', 'logistf', 'phylolm', 'ggplot2',
  'ggridges', 'DHARMa', 'rr2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'chron', 'stringr', 'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'RSQLite', 'DBI', 'data.table', 'e1071', 'keras', 'randomForest',
  'reticulate', 'rms'
Running examples in 'PhysicalActivity-Ex.R' failed
The error most likely occurred in:

> ### Name: deliveryFeatures
> ### Title: Delivery Features
> ### Aliases: deliveryFeatures
> 
> ### ** Examples
> 
> data(deliveryData)
> 
> deliveryDataProcessed <- deliveryPreprocess(df = deliveryData)
Warning in deliveryPreprocess(df = deliveryData) :
  .id unspecified - dummy ID created
> deliveryDataFeats <- deliveryFeatures(df = deliveryDataProcessed)
Error: deliveryFeatures requires the e1071 package, please install it.
Execution halted
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'childsds', 'dplyr', 'ggplot2', 'lintr', 'magrittr', 'rmarkdown',
  'testthat', 'knitr', 'spelling', '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: 'phytools', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'maps', 'clusterGeneration', 'coda', 'combinat', 'expm',
  'gtools', 'mnormt', 'numDeriv', 'phangorn', 'plotrix',
  'scatterplot3d'

Packages suggested but not available for checking:
  'animation', 'geiger', 'RColorBrewer', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'insol', 'FME'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'vegan'

Packages suggested but not available for checking:
  'brglm', 'circular', 'corpcor', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'png', 'FrF2', 'DoE.base', 'FrF2.catlg128'

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:
  'backports', 'gridGeometry', 'grImport2', 'purrr', 'jpeg', 'png',
  'R6', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'magick', 'rayrender', 'rgl', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'DiagrammeR', 'emmeans', 'igraph', 'lme4', 'multcomp'

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:
  'gh', 'httr', 'jsonlite', 'git2r', 'fs', 'usethis', 'crayon',
  'clisymbols', 'magrittr', 'lubridate', 'memoise'

Packages suggested but not available for checking:
  'spelling', 'readr', 'covr', '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'

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:
  'cli', 'crayon', 'ellipsis', 'fansi', 'lifecycle', 'rlang', 'utf8',
  'vctrs'

Packages suggested but not available for checking:
  'bit64', 'debugme', 'DiagrammeR', 'dplyr', 'ggplot2', 'knitr',
  'lubridate', 'nycflights13', 'palmerpenguins', 'rmarkdown', 'scales',
  'stringi', 'testthat', 'tibble', '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:
  'Rcpp', 'ggplot2', 'scales', '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: 'nleqslv', 'BB'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fastcluster', 'lubridate', 'ggplot2', 'reshape2', 'scales', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'formatR'

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', 'stringr', 'tibble', 'tictoc', 'tidyselect', 'data.table',
  'lubridate', 'plotly', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'processx'

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:
  'data.table', 'openssl', 'magrittr', 'purrr', 'uuid', 'httr',
  'jsonlite', 'rjson'

Packages suggested but not available for checking: 'testthat', 'yaml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'odds.converter', 'tidyverse', 'pinnacle.API', 'Lahman'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'knitr', 'lubridate', 'rmarkdown',
  'rnaturalearthdata', 'sf', 'tidyverse', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 2048 marked UTF-8 strings
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.
Packages required but not available:
  'foreach', 'entropy', 'doParallel', 'matrixStats', 'Rcpp',
  'RcppParallel', 'FNN', 'irlba', 'mclust', 'RcppArmadillo'

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:
  'backports', 'base64enc', 'crayon', 'digest', 'filelock', 'fs',
  'httr', 'jsonlite', 'magrittr', 'mime', 'openssl', 'rappdirs',
  'withr', 'yaml', 'zip'

Packages suggested but not available for checking:
  'callr', 'covr', 'data.table', 'knitr', 'rmarkdown', 'R6', 'stringi',
  'tibble', '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: 'splitstackshape', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gtools', 'xtable'

Package suggested but not available for checking: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'miniUI', 'rstudioapi', 'shiny', '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:
  'knitr', 'testthat', 'rmarkdown', 'modelr', 'tidyverse'

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: 'checkmate'

Packages suggested but not available for checking: 'testthat', 'covr'

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
plot.pred.int: no visible global function definition for 'plot.default'
plot.pred.int: no visible global function definition for 'axis'
plot.pred.int: no visible global function definition for 'box'
plot.pred.int : cidist: no visible global function definition for
  'ecdf'
plot.pred.int : negcidist: no visible global function definition for
  'ecdf'
plot.pred.int : pi.col.fun: no visible global function definition for
  'gray'
plot.pred.int: no visible global function definition for 'segments'
plot.pred.int: no visible global function definition for 'points'
plot.pred.int: no visible global function definition for 'abline'
pred.int: no visible binding for global variable 'sd'
prop.test.mult: no visible global function definition for 'qnorm'
sim.basic: no visible global function definition for 'rbinom'
sim.basic: no visible global function definition for 'rnorm'
t.test.mult: no visible global function definition for 'qt'
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Packages required but not available:
  'plyr', 'ggplot2', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'rmarkdown'

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.
Package required but not available: 'Rdpack'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'foreach', 'doParallel', 'hdrcde',
  'rfinterval', 'ranger'

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: 'ggplot2', 'XML2R', 'plyr', 'hexbin'

Packages suggested but not available for checking:
  'DBI', 'dplyr', 'RSQLite', 'knitr', 'animation', 'shiny', 'testthat',
  'ggsubplot', 'rgl'

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:
  'mclust', 'corpcor', 'runjags', 'rstan', 'bayesmix', 'rjags',
  'mvtnorm', 'RcmdrMisc', 'bayesplot'

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: 'semver'

Packages suggested but not available for checking:
  'DBI', 'RPostgreSQL', 'shiny', 'testthat', 'randomForest',
  'topicmodels'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr'

Packages suggested but not available for checking:
  'httptest', 'knitr', 'magrittr', '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:
  'R6', 'dplyr', 'data.table', 'htmltools', 'htmlwidgets'

Packages suggested but not available for checking:
  'ggplot2', 'jsonlite', 'lubridate', 'listviewer', 'openxlsx',
  'basictabler', 'shiny', '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: 'tibble'

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: 'beepr', 'cli', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'shiny', 'miniUI'

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', 'checkmate', 'htmltools', 'knitr', 'labelVector',
  'magrittr', 'reshape2', 'scales'

Packages suggested but not available for checking:
  'dplyr', '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', 'shinythemes', 'shinydashboard'

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:
  'callr', 'cli', 'crayon', 'desc', 'prettyunits', 'R6', 'rprojroot',
  'withr'

Packages suggested but not available for checking:
  'Rcpp', 'cpp11', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'callr', 'cli', 'curl', 'digest', 'filelock', 'glue',
  'jsonlite', 'prettyunits', 'R6', 'processx', 'rappdirs', 'rlang',
  'tibble', 'uuid'

Packages suggested but not available for checking:
  'covr', 'debugme', 'desc', 'fs', 'mockery', 'pingr', 'rprojroot',
  'sessioninfo', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'testthat'

Package which this enhances but not available for checking: 'assertthat'
Package unavailable to check Rd xrefs: 'assertthat'
'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 suggested but not available for checking:
  'covr', 'testthat', 'disposables'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'callr', 'cli', 'crayon', 'curl', 'desc', 'filelock', 'glue',
  'jsonlite', 'lpSolve', 'pkgbuild', 'pkgcache', 'prettyunits',
  'processx', 'ps', 'rematch2', 'rprojroot', 'R6', 'tibble', 'withr',
  'zip'

Packages suggested but not available for checking:
  'asciicast', 'debugme', 'digest', 'fansi', 'fs', 'htmlwidgets',
  'mockery', 'pingr', 'rlang', 'rstudioapi', 'spelling', 'testthat',
  'webfakes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'crayon', 'desc', 'digest', 'downlit', 'fs', 'httr',
  'magrittr', 'memoise', 'openssl', 'purrr', 'ragg', 'rematch2',
  'rlang', 'rmarkdown', 'tibble', 'whisker', 'withr', 'xml2', 'yaml'

Packages suggested but not available for checking:
  'covr', 'htmlwidgets', 'jsonlite', 'knitr', 'leaflet', 'pkgload',
  'testthat', 'rticles', 'rsconnect', 'rstudioapi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'downloader', 'rappdirs'

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:
  'ggnetwork', 'ggplot2', 'data.table', 'curl', 'dplyr', 'htmltools',
  'igraph', 'intergraph', 'networkD3', 'network', 'RColorBrewer',
  'tibble', 'plyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'magrittr', 'sna', 'statnet.common',
  'BiocManager'

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:
  'whoami', 'tinytest', 'roxygen2'
Package unavailable to check Rd xrefs: 'whoami'
Packages required but not available: 'cli', 'magrittr', 'remotes'

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:
  'cli', 'crayon', 'desc', 'rlang', 'rprojroot', 'rstudioapi', 'withr'

Packages suggested but not available for checking:
  'bitops', 'covr', 'pkgbuild', 'Rcpp', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'registry', 'digest', 'stringr', 'xtable', 'withr', 'assertthat'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'RUnit', 'testthat', 'knitr', 'rmarkdown',
  'markdown', 'yaml', 'Biobase', 'rbibutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ComplexHeatmap', 'GetoptLong', 'crayon', 'callr'

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', 'covr', 'data.table', 'DT', 'futile.logger', 'glue',
  'igraph', 'knitr', 'magrittr', 'R6', 'rlang', 'rmarkdown',
  'visNetwork'

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'testthat', 'webshot', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'commonmark', 'httr', 'xml2', '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:
  'assertthat', 'curl', 'jsonlite', 'parsedate', 'prettyunits',
  'tibble'

Packages suggested but not available for checking:
  'mockery', 'covr', 'memoise', 'pingr', 'rstudioapi', 'shiny',
  'shinyjs', 'shinyWidgets', 'testthat', 'whoami'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'base64enc'

Package which this enhances but not available for checking: 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'digest', 'rlang', 'tidyr'

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.
PKmod: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Package required but not available: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'binr', 'forestplot', 'rtf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'data.table', 'deSolve', 'dplyr', 'getPass', 'magrittr',
  'foreach', 'doParallel', 'reshape'

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: 'sets'

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', 'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'placer-Ex.R' failed
The error most likely occurred in:

> ### Name: plastic.ci
> ### Title: Confidence intervals of plastic prevalence probability
> ### Aliases: plastic.ci
> 
> ### ** Examples
> 
> plastic.ci(rbinom(1000,1,0.5), 30, 100)
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: plastic.ci ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'sp', 'rgdal', 'geosphere', 'data.table', 'rlang',
  'googleway', 'stringr', 'hms'

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:
  'CVXR', 'igraph', 'partykit', 'psychotools', 'psychotree', 'R6',
  'RSpectra', 'qvcalc', 'sandwich'

Packages suggested but not available for checking:
  'BiocStyle', 'BayesMallows', 'BradleyTerry2', 'PLMIX', 'ROlogit',
  'StatRank', 'bookdown', 'covr', 'hyper2', 'kableExtra', 'knitr',
  'lbfgs', 'gnm', 'pmr', 'prefmod', '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', '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:
  'gdalUtils', 'htmltools', 'htmlwidgets', 'png', 'raster',
  'viridisLite'

Packages suggested but not available for checking: 'shiny', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dielectric', 'Rcpp', 'statmod', 'cubature', 'reshape2', 'plyr',
  'ggplot2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'Hmisc', 'gridExtra', '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:
  'R6', 'stringr', 'gsl', 'uniformly', 'sdpt3r'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'viridisLite', 'sets', 'ellipse'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 150 marked UTF-8 strings
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:
  'nlstools', 'testthat', 'knitr', 'rmarkdown', 'DT'

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:
  'ggplot2', 'minpack.lm', 'plantecophys', '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: 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'GenomicRanges', 'VariantAnnotation', 'S4Vectors',
  'Rsamtools', 'rtracklayer', 'robustbase', 'SummarizedExperiment'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'dplyr', 'gdata', 'ggdendro', 'ggplot2', 'gridExtra',
  'gtable', 'htmlwidgets', 'magrittr', 'plotly', 'plyr',
  'RColorBrewer', 'reshape2', 'stringr'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glm2', 'arm', 'lme4', 'twang', 'gbm', 'survey', 'xtable',
  'latticeExtra', 'RColorBrewer', 'epiDisplay'

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:
  '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: 'RColorBrewer', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'rms'

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', 'RColorBrewer', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'limma', 'RGtk2', 'gWidgets2', 'gWidgets2RGtk2', 'cairoDevice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sfsmisc', 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'tgp'

Packages suggested but not available for checking:
  'ellipse', 'splancs', 'akima'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'optparse', 'data.table', 'R.utils', 'ggplot2', 'ggforce', 'ggrepel',
  'cowplot', 'UpSetR', 'dplyr', 'igraph', 'sys'

Packages suggested but not available for checking:
  'testthat', 'mockery', '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: 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bwfw.hmm: no visible global function definition for 'dnorm'
bwfw1.hmm: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Packages required but not available: 'lme4', 'numDeriv', 'optimx'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'irtoys'

VignetteBuilder 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', 'abind', 'foreach', 'ggplot2', 'ggmcmc', 'coda', 'reshape2',
  'rcdd', 'gridExtra', 'MCMCpack', 'gtools', 'label.switching',
  'radarchart', 'prefmod', 'rankdist', 'StatRank', 'pmr',
  'PlackettLuce'

Package suggested but not available for checking: 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sm', 'Formula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bdsmatrix', 'zoo', 'sandwich', 'lmtest', 'maxLik', 'Rdpack',
  'Formula'

Packages suggested but not available for checking:
  'AER', 'car', 'pcse', 'clusterSEs', 'collapse', 'pglm', 'spdep',
  'splm', 'statmod', 'urca', 'Ecdat', 'pder', 'stargazer', 'texreg',
  'knitr', 'rmarkdown', '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:
  'future', 'future.apply', 'R6', 'glassoFast', 'Rcpp', 'nloptr',
  'igraph', 'gridExtra', 'dplyr', 'tidyr', 'purrr', 'ggplot2',
  'corrplot', 'magrittr', 'rlang', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'pkgdown', 'biomformat',
  'phyloseq', 'spelling', 'factoextra', 'Wrench'

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: 'Rcpp'
'LazyData' is specified without a 'data' directory
Running examples in 'plogr-Ex.R' failed
The error most likely occurred in:

> ### Name: plogr-package
> ### Title: plogr: The 'plog' C++ Logging Library
> ### Aliases: plogr plogr-package
> 
> ### ** Examples
> 
> plogr_demo <- Rcpp::cppFunction(depends = "plogr", '
+ // C++ code begin
+ #include <plogr.h>
+ 
+ RObject plogr_demo() {
+   plog::init_r(plog::info);
+   LOG_INFO << "shown";
+   LOG_DEBUG << "not shown";
+   plog::init_r("DEBUG");
+   LOG_DEBUG << "shown now";
+   return R_NilValue;
+ }
+ 
+ #include <Rcpp.h> // not necessary to use plogr
+ // C++ code end
+ '
+ )
Error in loadNamespace(x) : there is no package called 'Rcpp'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'misc3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'plot3D'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggtern', 'Ternary', 'dplyr', 'ellipse', 'forcats', 'generics',
  'ggplot2', 'lifecycle', 'magrittr', 'purrr', 'Rdpack', 'stringr',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'knitr', 'mlogit', 'ordinal', 'rmarkdown', 'VGAM', '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:
  'cmocean', 'dplyr', 'gganimate', 'ggnewscale', 'ggplot2', 'lazyeval',
  'lubridate', 'magrittr', 'maps', 'raster', 'rerddap', 'rgeos',
  'scales', 'sf', 'tidyr', 'viridis'

Packages suggested but not available for checking:
  'Cairo', 'knitr', 'mapdata', 'maptools', 'rgdal', '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', 'sp'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'wesanderson', 'amerika', 'ggplot2'

Packages suggested but not available for checking: 'mixtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'ggfittext', 'magick', 'gridExtra', 'scales',
  'farver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'XML', 'landmap', 'sp', 'raster', 'rgdal', 'aqp', 'gstat',
  'spacetime', 'colorspace', 'plotrix', 'dismo', 'pixmap', 'plyr',
  'stringr', 'colorRamps', 'scales', 'zoo', 'RColorBrewer', 'RSAGA',
  'classInt', 'sf', 'stars'

Packages suggested but not available for checking:
  'adehabitatLT', 'maptools', 'fossil', 'rjson', 'animation',
  'spatstat', 'spatstat.linnet', 'spatstat.geom', 'RCurl', 'rgbif',
  'Hmisc', 'uuid', 'intervals', 'reshape', 'gdalUtils', 'snowfall',
  'tinytex', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Hmisc', 'quantreg', 'scales', 'plyr', 'hexbin', 'RColorBrewer',
  'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'ggplot2movies', 'knitr', 'rmarkdown', 'gapminder'

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', 'htmltools'

Package which this enhances but not available for checking: 'plotly'
'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', 'scales', 'httr', 'jsonlite', 'magrittr', 'digest',
  'viridisLite', 'base64enc', 'htmltools', 'htmlwidgets', 'tidyr',
  'RColorBrewer', 'dplyr', 'vctrs', 'tibble', 'lazyeval', 'rlang',
  'crosstalk', 'purrr', 'data.table', 'promises'

Packages suggested but not available for checking:
  'maps', 'hexbin', 'ggthemes', 'GGally', 'testthat', 'knitr',
  'devtools', 'shiny', 'shinytest', 'curl', 'rmarkdown', 'vdiffr',
  'Cairo', 'broom', 'webshot', 'listviewer', 'dendextend', 'sf',
  'maptools', 'rgeos', 'png', 'IRdisplay', 'processx',
  'plotlyGeoAssets', 'forcats', 'palmerpenguins'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'psych'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'plot.matrix-Ex.R' failed
The error most likely occurred in:

> ### Name: bfi.2
> ### Title: 25 Personality items representing 5 factors
> ### Aliases: bfi.2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(bfi.2)
> library("psych")
Error in library("psych") : there is no package called 'psych'
Execution halted
Packages required but not available: 'coda', 'gplots'

Package suggested but not available for checking: 'gdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'interactionTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wesanderson', 'amerika', 'ggplot2', 'dplyr', 'patchwork'

Packages suggested but not available for checking:
  'mixtools', 'EMCluster', 'flexmix', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'plotrix', 'TeachingDemos'

Packages suggested but not available for checking:
  'C50', 'earth', 'gbm', 'glmnet', 'glmnetUtils', 'mlr', 'neuralnet',
  'partykit', 'pre', 'rpart.plot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'reshape2', 'ggplot2'

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.
Malformed Title field: should not end in a period.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'gridSVG', 'shiny', 'plyr', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'stringr', 'survivalROC', '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'

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', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'plyr', 'shiny', 'MplusAutomation', 'Rcpp', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'knitr'
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.
llla.bi: no visible global function definition for 'as.formula'
llla.bi: no visible global function definition for 'glm'
llla.bi: no visible global function definition for 'binomial'
llla.bi: no visible binding for global variable 'logit'
llla.bi: no visible global function definition for 'vcov'
llla.bi: no visible global function definition for 'coef'
llla.mc: no visible global function definition for 'model.matrix'
llla.mc: no visible global function definition for 'as.formula'
llla.mc: no visible global function definition for 'coxph'
llla.mc: no visible global function definition for 'vcov'
llla.mc: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'as.formula'
llla.mle: no visible global function definition for 'glm'
llla.mle: no visible global function definition for 'poisson'
llla.mle: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'vcov'
mclgen: no visible global function definition for 'reshape'
simRasch.1D: no visible global function definition for 'rnorm'
simRasch.1D: no visible global function definition for 'runif'
vcov.sandwich.glm: no visible global function definition for
  'model.matrix'
vcov.sandwich.glm: no visible global function definition for 'weights'
vcov.sandwich.glm: no visible global function definition for
  'residuals'
vcov.sandwich.glm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'chemometrics', 'mixOmics', 'mvabund', 'pls', 'plsgenomics',
  'robustbase', 'SensoMineR'
Running examples in 'PLSbiplot1-Ex.R' failed
The error most likely occurred in:

> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pls'
> X = as.matrix(oliveoil$chemical, ncol=5)
Error in as.matrix(oliveoil$chemical, ncol = 5) : 
  object 'oliveoil' not found
Execution halted
Packages suggested but not available for checking: 'FactoMineR', 'plspm'
Packages required but not available:
  'reshape2', 'plyr', 'fields', 'RhpcBLASctl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'parsnip', 'tibble', 'mixOmics', 'dplyr', 'tidyr', 'generics',
  'magrittr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'modeldata', 'testthat', 'covr', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'glmnet'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', '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:
  'mvtnorm', 'Formula', 'plsRglm', 'betareg'

Packages suggested but not available for checking: 'pls', 'plsdof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Rmpi', 'testthat', 'RUnit'
Package unavailable to check Rd xrefs: 'sm'
Running 'test_import.R'
Running the tests in 'tests/test_import.R' failed.
Last 13 lines of output:
  > ## Get warnings at once
  > options(warn = 1)
  > 
  > ## Make sure the global environment is clean:
  > rm(list = ls(all = TRUE))
  > 
  > ## Get the data
  > data(yarn, package = "pls")
  > data(oliveoil, package = "pls")
  > data(gasoline, package = "pls")
  > 
  > ## Get RUnit and utility functions
  > library(RUnit)
  Error in library(RUnit) : there is no package called 'RUnit'
  Execution halted
Packages required but not available:
  'plsRglm', 'lars', 'pls', 'kernlab', 'mixOmics', 'risksetROC',
  'survcomp', 'survAUC', 'rms'

Packages suggested but not available for checking: 'survivalROC', 'plsdof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'bipartite', 'car'

Packages suggested but not available for checking:
  'plsdof', 'R.rsp', 'chemometrics', 'plsdepot'

Package which this enhances but not available for checking: 'pls'

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: 'ggplot2', 'reshape2', '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:
  'pls', 'genalg', 'mvtnorm', 'bdsmatrix', 'progress', 'MSQC',
  'praznik'

Package suggested but not available for checking: 'Rmpi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coreSim', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Packages required but not available:
  'analogsea', 'ssh', 'jsonlite', 'lifecycle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'stringi', 'jsonlite', 'webutils', 'httpuv', 'crayon',
  'promises', 'sodium', 'swagger', 'magrittr', 'mime', 'lifecycle',
  'ellipsis', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'base64enc', 'htmlwidgets', 'visNetwork',
  'later', 'readr', 'yaml', 'feather', 'future', 'rstudioapi',
  'spelling', 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'objectSignals'

Packages suggested but not available for checking: 'plyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

Packages suggested but not available for checking:
  'tinytest', '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: 'backports', 'lifecycle'

Packages suggested but not available for checking:
  'covr', 'crayon', 'fracture', 'nombre', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RCurl', 'RJSONIO', 'lubridate', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'abind', 'covr', 'doParallel', 'foreach', 'iterators', 'itertools',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reticulate', 'bupaR', 'petrinetR', 'purrr', 'stringr'

Packages suggested but not available for checking: 'testthat', 'eventdataR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mixture', 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pbdMPI'

Package which this enhances but not available for checking: 'MixSim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'multcompView', 'gmp', 'Rmpfr', 'SuppDists', 'kSamples',
  'BWStest'

Packages suggested but not available for checking:
  'xtable', 'knitr', 'rmarkdown', 'car', 'e1071', 'multcomp', 'pwr',
  'NSM3'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'multcompView', 'xtable'
Packages unavailable to check Rd xrefs: 'multcompView', 'xtable'
Running examples in 'PMCMR-Ex.R' failed
The error most likely occurred in:

> ### Name: get.pvalues
> ### Title: Prints PMCMR objects
> ### Aliases: get.pvalues
> ### Keywords: utilities
> 
> ### ** Examples
> 
> data(InsectSprays)
> attach(InsectSprays)
> out <- posthoc.kruskal.dunn.test(count ~ spray, p.adjust="bonf")
Warning in posthoc.kruskal.dunn.test.default(c(10, 7, 20, 14, 14, 12, 10,  :
  Ties are present. z-quantiles were corrected for ties.
> out.p <- get.pvalues(out)
> out.p
         A-B          A-C          A-D          A-E          A-F          B-C 
1.000000e+00 2.707991e-05 2.735271e-02 1.767898e-03 1.000000e+00 5.462003e-06 
         B-D          B-E          B-F          C-D          C-E          C-F 
9.043735e-03 4.705845e-04 1.000000e+00 1.000000e+00 1.000000e+00 3.334462e-06 
         D-E          D-F          E-F 
1.000000e+00 6.396937e-03 3.120186e-04 
> 
> ### a barplot, significant level at p < 0.05
> require(multcompView)
Loading required package: multcompView
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'multcompView'
> out.mcV <- multcompLetters(out.p, threshold=0.05)
Error in multcompLetters(out.p, threshold = 0.05) : 
  could not find function "multcompLetters"
Execution halted
Errors in running code in vignettes:
when running code in 'PMCMR.Rnw'
  ...
Warning in posthoc.kruskal.dunn.test.default(c(10, 7, 20, 14, 14, 12, 10,  :
  Ties are present. z-quantiles were corrected for ties.

> out.p <- get.pvalues(out)

> out.mcV <- multcompLetters(out.p, threshold = 0.05)

  When sourcing 'PMCMR.R':
Error: could not find function "multcompLetters"
Execution halted

  'PMCMR.Rnw' using 'UTF-8'... failed
Packages required but not available:
  'dplyr', 'geiger', 'ggplot2', 'ouch', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'gridExtra', '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:
  'dplyr', 'lubridate', 'magrittr', 'pillar', 'tidyr', 'tibble',
  'tidyselect', 'vctrs', 'rlang'

Packages suggested but not available for checking:
  'tsibble', 'plm', 'panelr', 'haven', 'utf8', 'sjlabelled', '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:
  'RColorBrewer', 'data.table', 'igraph', 'enviGCMS'

Packages suggested but not available for checking:
  'knitr', 'shiny', 'rmarkdown', 'MSnbase'

VignetteBuilder 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', 'httr', 'lubridate', 'magrittr', 'RCurl', 'tidyr', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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: 'mvtnorm', 'Quandl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FNN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'rbokeh', 'dplyr', '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: 'XML', 'stringr'

Packages suggested but not available for checking:
  'ada', 'amap', 'arules', 'caret', 'clue', 'data.table', 'forecast',
  'gbm', 'glmnet', 'neighbr', 'randomForestSRC', 'randomForest',
  'rattle', 'kernlab', 'e1071', 'testthat', 'xgboost', 'knitr',
  'rmarkdown', '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', 'testthat', 'rmarkdown', 'pmml'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'pmml'
Running examples in 'pmmlTransformations-Ex.R' failed
The error most likely occurred in:

> ### Name: DiscretizeXform
> ### Title: Discretizes a continuous variable to a discrete one as indicated
> ###   by interval mappings. This is in accordance to the PMML element:
> ###   *Discretize*
> ### Aliases: DiscretizeXform
> ### Keywords: manip
> 
> ### ** Examples
> 
> # Load the pmmlTransformations package
>     library(pmmlTransformations)
>     library(pmml)
Error in library(pmml) : there is no package called 'pmml'
Execution halted
Packages required but not available:
  'plm', 'pracma', 'minqa', 'dplyr', 'data.table', 'moments',
  'magrittr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dbm: no visible global function definition for 'optim'
dbm: no visible global function definition for 'new'
destat: no visible global function definition for 'weighted.mean'
local.knn: no visible global function definition for 'sd'
local.knn: no visible global function definition for 'optim'
mdpref: no visible global function definition for 'sd'
mdpref: no visible global function definition for 'text'
mdpref: no visible global function definition for 'lines'
phicom: no visible global function definition for 'optim'
phicom: no visible global function definition for 'new'
pl: no visible global function definition for 'optim'
pl: no visible global function definition for 'new'
rol: no visible global function definition for 'nlm'
rol: no visible global function definition for 'new'
wdbm: no visible global function definition for 'optim'
wdbm: no visible global function definition for 'new'
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
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: 'fftw'

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', 'coda', 'condMVNorm', 'MCMCpack', 'mvtnorm'

Packages suggested but not available for checking:
  'covr', 'rtdists', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'NMOF', 'datetimeutils', 'fastmatch', 'orgutils', 'textutils', 'zoo'

Packages suggested but not available for checking:
  'crayon', 'rbenchmark', 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'magrittr', 'data.tree', 'DiagrammeR', 'ggplot2',
  'ggrepel', 'gridExtra', 'chron', 'xml2', '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 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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'rgenoud'
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud
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.
Package suggested but not available for checking: 'ggplot2'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tibble', 'pracma', 'nloptr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'purrr', 'tibble', 'dplyr', 'glue', 'jsonlite', 'magrittr',
  'usethis'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'covr', 'httptest', '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: 'ggplot2', 'pracma', 'EbayesThresh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dfcrm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DBI', 'assertthat', 'dplyr', 'lubridate', 'magrittr', 'odbc',
  'plogr', 'rstudioapi', 'shiny', 'stringr', 'tibble', 'RPostgres'

Packages suggested but not available for checking:
  'DT', 'haven', 'huxtable', 'knitr', 'kableExtra', 'pharmaRTF',
  'rmarkdown', 'readr', 'shinyBS', 'shinydashboard', 'shinyjs',
  'testthat', '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:
  'abc', 'doParallel', 'foreach', 'gdistance', 'geosphere', 'lhs',
  'metRology', 'R6', 'raster', 'trend'

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', 'PUlasso', 'glmnet', 'pROC', 'RcppArmadillo'

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.
Packages required but not available: 'ggplot2', 'logistf', 'plyr'

Package suggested but not available for checking: 'COUNT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'SmarterPoland'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
bipoilogMLE: no visible global function definition for 'optim'
bipoilogMLE: no visible global function definition for 'write.table'
poilogMLE: no visible global function definition for 'optim'
rbipoilog : sim: no visible global function definition for 'rnorm'
rbipoilog : sim: no visible global function definition for 'rpois'
rpoilog : sim: no visible global function definition for 'rnorm'
rpoilog : sim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'base64enc', 'blastula', 'cli', 'DBI', 'digest', 'dplyr', 'dbplyr',
  'fs', 'glue', 'gt', 'htmltools', 'knitr', 'rlang', 'magrittr',
  'scales', 'testthat', 'tibble', 'tidyr', 'tidyselect', 'yaml'

Packages suggested but not available for checking:
  'arrow', 'covr', 'crayon', 'duckdb', 'ggforce', 'ggplot2',
  'jsonlite', 'log4r', 'lubridate', 'RSQLite', 'RMySQL', 'RPostgres',
  'readr', 'rmarkdown', 'sparklyr', 'dittodb', 'odbc'

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:
  'gmm', 'car', 'ggplot2', 'lubridate', 'sandwich'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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: 'rARPACK', 'CompQuadForm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridExtra', 'plyr', 'TripleR'

Packages suggested but not available for checking:
  'dplR', '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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive.base', 'assertive.properties', 'assertive.types',
  'assertive.files', 'assertive.sets', 'assertive.strings', 'devtools',
  'digest', 'dplyr', 'magrittr', 'purrr', 'R6', 'stringi', 'tibble',
  'whoami'

Packages suggested but not available for checking:
  'testthat', 'rebus.datetimes'

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.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'corpcor', 'GenOrd', 'BB'

Package suggested but not available for checking: 'moments'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'corpcor', 'mvtnorm', 'psych', 'GenOrd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'corpcor', 'GenOrd', '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: 'data.table', 'glmmML'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'SparseM'
Packages required but not available: 'BB', 'corpcor'

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.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  '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: 'robustbase', 'robcbi', 'checkmate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'parsnip', 'rlang', 'tibble', 'purrr', 'dplyr', 'tidyr', 'glue'

Packages suggested but not available for checking:
  'testthat', 'pscl', 'covr', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'combinat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'argonDash', 'argonR', 'colourpicker', 'ggplot2', 'hexSticker',
  'png', 'shiny', 'shinyWidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'vegan', 'ineq', 'reshape2'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'rmarkdown', '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: 'Rcpp', 'grf', 'BH'

Packages suggested but not available for checking: 'testthat', 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'descr', 'Hmisc', 'weights', 'plyr', 'gplots', 'xtable', 'survey',
  'car', 'plotrix', 'abind'

Packages suggested but not available for checking:
  'hexbin', 'rgl', 'scatterplot3d', 'R2HTML', 'gdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'automagic', 'cli', 'digest', 'dplyr', 'DT', 'htmltools', 'httr',
  'jose', 'jsonlite', 'lubridate', 'purrr', 'R6', 'rlang', 'shiny',
  'shinycssloaders', 'shinydashboard', 'shinyFeedback', 'shinyjs',
  'shinyWidgets', 'stringr', 'tibble', 'tidyr', 'uuid', '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:
  'tm', 'quanteda', 'ggplot2', 'spacyr', 'textir', 'glmnet',
  'data.table', 'stringr', 'stringi'

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:
  'here', 'httr', 'magrittr', 'memoise', 'ratelimitr', 'robotstxt',
  'rvest', 'usethis'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lubridate', 'purrr', 'dplyr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'tidyr', '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: 'brms', 'repmis'

Packages suggested but not available for checking:
  'rstan', 'pollimetrydata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'stringr', 'tidyr', 'labelled', 'forcats', 'rlang'

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:
  'httr', 'lubridate', 'purrr', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'jsonlite', 'knitr', 'readr', '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:
  'data.table', 'slam', 'tm', 'DT', 'xml2', 'stringi', 'jsonlite',
  'pbapply', 'RcppCWB', 'magrittr', 'knitr'

Packages suggested but not available for checking:
  'markdown', 'rmarkdown', 'htmltools', 'highlight', 'sendmailR',
  'shiny', 'shinythemes', 'miniUI', 'rhandsontable', 'testthat',
  'tidytext', 'covr', 'igraph', 'NLP', 'httr', 'protolite', 'curl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
qPolyaAeppliSingle: no visible global function definition for 'qgamma'
rPolyaAeppli: no visible global function definition for 'rpois'
rPolyaAeppli: no visible global function definition for 'rgeom'
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
Package required but not available: 'rcdd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'colorspace', 'scatterplot3d'

Packages suggested but not available for checking:
  'RColorBrewer', 'knitr', 'rmarkdown', 'ggplot2'

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: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sp'

Packages suggested but not available for checking:
  'spatstat.geom', 'mvtnorm', 'statmod', 'rgeos', 'gpclib', 'sf',
  'cubature', 'knitr', 'rmarkdown', 'microbenchmark'

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: 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'coda'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magick', 'pins'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'XML'

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:
  'covr', 'testthat', 'spelling', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'igraph', 'knitr', 'MDSMap'

Packages suggested but not available for checking:
  'ggplot2', 'hexbin', 'Hmisc', 'RColorBrewer', 'reshape2',
  'rmarkdown', 'polyRAD', 'updog', 'mappoly'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MTS', 'polynom'

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: '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'
Package required but not available: 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'impute', 'pcaMethods', 'xlsx', 'imputeLCMD', 'plyr', 'sqldf',
  'gplots', 'corrplot', 'circlize', 'mixOmics', 'pkr', 'Hmisc', 'ropls'

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:
  'tibble', 'reshape2', 'ggplot2', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'lme4'

VignetteBuilder 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', 'doParallel', 'foreach', 'Hmisc', 'knitr', 'RColorBrewer',
  'Rcpp', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'igraph', 'mappoly', 'polymapR', '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: 'fastmatch', 'pcaMethods', 'Rcpp'

Packages suggested but not available for checking:
  'rrBLUP', 'Rsamtools', 'GenomeInfoDb', 'Biostrings', 'GenomicRanges',
  'VariantAnnotation', 'SummarizedExperiment', 'S4Vectors', 'IRanges',
  'BiocGenerics', 'knitr', 'rmarkdown', 'GenomicFeatures', 'qqman',
  'ggplot2', 'adegenet'

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:
  'dummies', 'partools', 'regtools', 'RSpectra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'ade4', 'adegenet', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'polySegratio', 'gtools', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'miscTools', 'foreach', 'Formula', 'glmnet', 'iterators', 'ncvreg',
  'Rcpp', 'stringr'

Packages suggested but not available for checking: 'carData', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'matrixStats', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'visNetwork', 'Ternary'

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:
  'lavaan', 'ggplot2', 'reshape2', 'qgraph'

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:
  'digest', 'mvtnorm', 'deSolve', 'coda', 'reshape2', 'magrittr',
  'plyr'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'tidyr', 'dplyr', 'subplex', 'nloptr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'matrixcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glue'

Packages suggested but not available for checking:
  'testthat', 'covr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'doParallel', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cubature', 'data.table', 'dplyr', 'dvmisc', 'ggplot2', 'ggrepel',
  'mvtnorm', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DBI', 'R6', 'later'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'dplyr', 'dbplyr', 'RSQLite', 'RMySQL'

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:
  > ### to also run skip_on_cran() tests, uncomment:
  > #Sys.setenv(NOT_CRAN="true")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'Rcpp', 'rstan', 'rstantools', 'brms', 'lme4', 'stringr',
  'progress', 'BH', 'RcppEigen', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'EmpiricalBrownsMethod', 'Hmisc', 'ranger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'pkgdown', 'rmarkdown', 'roxygen2', 'tinytest'

VignetteBuilder package required for checking but not installed: 'knitr'
Package suggested but not available for checking: 'quadprog'
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'maps', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'expm', 'MCMCpack'

Packages suggested but not available for checking: 'knitr', 'magick'

VignetteBuilder 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', 'mvtnorm', 'dplyr', 'magrittr', 'purrr', 'stringr',
  'tibble', 'gtools'

Packages suggested but not available for checking:
  'testthat', 'Hmisc', 'GA', 'deSolve', 'Rcpp', 'shiny',
  'rhandsontable', 'knitr', 'rmarkdown', 'gridExtra', 'covr',
  'devtools', 'mrgsolve'

VignetteBuilder 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', 'data.table'

Packages suggested but not available for checking:
  'reshape2', 'testthat', 'knitr', 'rmarkdown', 'relsurv', 'ggplot2',
  'mstate', 'date', 'roxygen2', '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.
Package required but not available: 'ff'

Packages suggested but not available for checking:
  'bigmemory', 'BASIX', 'WhopGenome', 'BlockFeST'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'adegenet', 'RgoogleMaps', 'gap', 'calibrate', 'xtable',
  'plyr', 'dismo', 'reshape', 'ggplot2', 'R.utils', 'ade4', 'pegas',
  'genetics', 'rgdal', 'gdistance', 'vegan', 'sp', 'mmod', 'GGally',
  'data.table', 'raster'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/PopGenReportIntroduction.Rnw'
   'inst/doc/Tutorial_landgenreport.rnw'
   'inst/doc/Tutorial_optimizer.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RColorBrewer', 'RcppEigen'

Packages suggested but not available for checking:
  'BEDMatrix', 'testthat', 'knitr', 'rmarkdown', 'lfa', 'bnpsd'

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: 'plotrix'
asymmetricIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'lm'
bonferroniIntervals: no visible global function definition for
  'predict'
bootstrapIntervals: no visible global function definition for 'stack'
component1a: no visible global function definition for 'pnorm'
component1b: no visible global function definition for 'pnorm'
component2: no visible global function definition for 'dgamma'
eqnForMin: no visible global function definition for 'pnorm'
eqnForMin: no visible global function definition for 'integrate'
integrand : <anonymous>: no visible global function definition for
  'pnorm'
integrand: no visible global function definition for 'dnorm'
integrate2: no visible global function definition for 'integrate'
integrate2a: no visible global function definition for 'integrate'
integrate2b: no visible global function definition for 'integrate'
integrate4a: no visible global function definition for 'integrate'
integrate4b: no visible global function definition for 'integrate'
optimalCScalar2: no visible global function definition for 'uniroot'
optimalLambda: no visible global function definition for 'optimise'
optimalLambdaC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
Errors in running code in vignettes:
when running code in 'popKorn.Rnw'
  ...

> asym.out <- asymmetricIntervals(Xmat, k = 3)

> bonf.out <- bonferroniIntervals(Xmat, k = 3)

> library(plotrix)

  When sourcing 'popKorn.R':
Error: there is no package called 'plotrix'
Execution halted

  'popKorn.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'popKorn.Rnw' using Sweave
Loading required package: boot

Error: processing vignette 'popKorn.Rnw' failed with diagnostics:
 chunk 5 (label = plot_intervals) 
Error in library(plotrix) : there is no package called 'plotrix'

--- failed re-building 'popKorn.Rnw'

SUMMARY: processing the following file failed:
  'popKorn.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'adegenet', 'vegan', 'ggplot2', 'ape', 'igraph', 'ade4', 'pegas',
  'polysat', 'dplyr', 'rlang', 'shiny', 'magrittr', 'progressr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'poweRlaw', 'cowplot', 'RClone'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/algo.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: 'knitr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coda'

Packages suggested but not available for checking:
  'ggplot2', 'reshape', 'gdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'ggplot2', 'hash'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'ggplot2', 'plyr', 'roxygen2', 'shiny', 'shinycssloaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BGLR', 'qtl', 'rrBLUP'

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: 'mvtnorm', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forecast', 'timetk', 'lubridate', 'xts', 'httr', 'tibble',
  'magrittr', 'zoo', 'curl', 'purrr'

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:
  'clipr', 'clisymbols', 'crayon', 'dplyr', 'forecast', 'gh', 'httr',
  'lubridate', 'lunar', 'magrittr', 'rlang', 'tidyr', 'tidyselect',
  'zoo'

Packages suggested but not available for checking:
  'covr', 'cowplot', 'ggplot2', 'httptest', 'knitr', 'pkgdown',
  '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: 'forecast'

Packages suggested but not available for checking:
  'akima', 'car', 'fGarch', 'FitAR', 'fracdiff', 'gstat', 'tseries',
  'vars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'xts', 'foreach', 'PerformanceAnalytics'

Packages suggested but not available for checking:
  'quantmod', 'DEoptim', 'iterators', 'fGarch', 'Rglpk', 'quadprog',
  'ROI', 'ROI.plugin.glpk', 'ROI.plugin.quadprog',
  'ROI.plugin.symphony', 'pso', 'GenSA', 'corpcor', 'testthat',
  'nloptr', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'evaluate', 'ggplot2', 'pbapply', 'PerformanceAnalytics',
  'quadprog', 'quantmod', 'R.utils', 'rlang', 'xts', 'zoo'

Packages suggested but not available for checking:
  'CVXR', 'DT', 'ggfortify', 'gridExtra', 'knitr', 'prettydoc',
  'readtext', 'rmarkdown', 'R.rsp', 'stringi', 'testthat'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'PortfolioEffectHFT', 'rJava'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rJava', '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: 'xts', 'magrittr', 'modopt.matlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rsymphony'

Packages suggested but not available for checking:
  'mvtnorm', 'Rglpk', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'zoo', 'MCMCpack', 'tseries', 'copula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'zoo'

Packages suggested but not available for checking:
  'PortfolioAnalytics', 'PerformanceAnalytics', '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', 'igraph', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rmarkdown', 'rstudioapi'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'knitr', 'dplyr', 'rmarkdown', 'testthat', 'covr', '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:
  'glmnet', 'grf', 'neuralnet', 'progress', 'ggplot2', 'doParallel'

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: 'pagedown', 'rmarkdown', 'yaml'

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:
  'dplyr', 'e1071', 'ggplot2', 'gridExtra', 'Rcpp', 'rstan',
  'StanHeaders', 'tibble'

Packages suggested but not available for checking:
  'knitr', '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:
  'refund', 'denseFLMM', 'dplyr', 'xlsx', 'tidyr', 'zoo', 'ineq',
  'cosinor', 'abind', 'accelerometry', 'minpack.lm', 'kableExtra',
  'GGIR'

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', 'DBI', 'jsonlite', 'rgdal', 'rgeos', 'RPostgreSQL', 'stringr'

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: 'igraph', 'multcomp'

Packages suggested but not available for checking:
  'xtable', 'lme4', '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
Packages required but not available:
  'tibble', 'crul', 'purrr', 'jsonlite', 'rvest', 'xml2'

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: '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:
  'stringr', 'matrixcalc', 'coda', 'mcmcse', 'abind'

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:
  'sf', 'isoband', 'doParallel', 'foreach'

Packages suggested but not available for checking:
  'covr', 'lwgeom', 'cartography', 'knitr', 'tinytest', '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: 'pooh'
Running 'cll.R'
  Comparing 'cll.Rout' to 'cll.Rout.save' ... OK
  Running 'debug-cond.R'
Running the tests in 'tests/debug-cond.R' failed.
Complete output:
  > 
  >  library(potts)
  >  library(pooh)
  Error in library(pooh) : there is no package called 'pooh'
  Execution halted
Package required but not available: 'miscF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'haplo.stats', 'gap', 'ggplot2', 'reshape2', 'BIGDAWG'

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', 'ape', 'data.table', 'coda', 'foreach', 'ggplot2', 'lamW',
  'adaptMCMC'

Packages suggested but not available for checking:
  'testthat', 'usethis', 'Rmpfr', 'mvtnorm', 'lmtest', 'knitr',
  'rmarkdown', 'doParallel'

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:
  'purrr', 'stringr', 'httr', 'jsonlite', 'readr', 'tibble', 'dplyr',
  'js', 'tidyr', 'naniar', 'memoise'

Packages suggested but not available for checking:
  'testthat', 'assertthat', 'knitr', 'rmarkdown', 'forcats', 'scales',
  'ggthemes', 'ggplot2', 'utf8', '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: 'broom', 'formula.tools'

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: 'rmutil', 'gamlss.dist', 'normalp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'reshape', 'plotly', 'ggplot2', 'ggpubr', 'shiny', 'DT',
  'nnls', 'shinyWidgets', 'baseline', 'tidyr'

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: 'PowerTOST', 'mvtnorm', 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'gdata', 'reshape2', 'stringr', 'plyr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GLMMadaptive', 'glmmTMB'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'pwr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'covr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'pracma'

Packages suggested but not available for checking:
  'covr', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/a_introduction.Rnw'
   'inst/doc/b_powerlaw_examples.Rnw'
   'inst/doc/c_comparing_distributions.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'scales'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'knitr', 'rmarkdown', 'pbmcapply',
  'lmerTest', 'ggplot2', 'ggsci', 'viridis', 'gridExtra', 'shiny',
  'shinydashboard'

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 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize pnorm points qnorm rexp rnorm uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Packages required but not available: 'complexplus', 'phonTools', 'expm'

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: 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'cubature', 'TeachingDemos'

Packages suggested but not available for checking:
  'crossdes', 'knitr', 'rmarkdown', 'devtools', 'tufte', 'emmeans'

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'
Package unavailable to check Rd xrefs: 'cosa'
Packages suggested but not available for checking: 'VGAM', 'nortest'
Packages unavailable to check Rd xrefs: 'nortest', 'VGAM'
Package required but not available: 'rARPACK'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'inaparc'

Packages suggested but not available for checking:
  'factoextra', 'fclust', 'knitr', 'rmarkdown', 'vegclust'

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: 'curl', 'tfse', 'jsonlite', '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:
  'dplyr', 'ggplot2', 'htmltools', 'htmlwidgets', 'leaflet',
  'magrittr', 'PakPC2017', 'rgdal', 'scales', 'shiny', 'tidyr', 'tmap'

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', '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
Packages required but not available:
  'Rcpp', 'magrittr', 'plyr', 'dplyr', 'tidyr', 'doParallel',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'gridExtra', 'GGally', 'ggplot2', 'RColorBrewer',
  'roxygen2', 'PPtreeViz', '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: 'evgam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'mclust', 'GA', 'ggplot2', 'ggthemes', 'cli', 'crayon',
  '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: 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'spelling', 'stringr', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nleqslv'

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: 'ggplot2', 'plotly'

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.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'eRm', 'data.table', '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: 'Rcpp', 'settings'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rfast', 'clue', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'parsnip', 'withr', 'gridExtra'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'circular', 'progress'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gridExtra', 'ggplot2', 'partykit', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'RColorBrewer', 'plyr', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'foreach', 'doParallel', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mclust'

Packages suggested but not available for checking:
  'spdep', 'spatialreg', 'bootstrap', 'maptools', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'NlcOptim', 'quadprog'
Running examples in 'pracma-Ex.R' failed
The error most likely occurred in:

> ### Name: fmincon
> ### Title: Minimize Nonlinear Constrained Multivariable Function.
> ### Aliases: fmincon
> ### Keywords: optimize
> 
> ### ** Examples
> 
> # Classical Rosenbrock function
> n <- 10; x0 <- rep(1/n, n)
> fn <- function(x) {n <- length(x)
+     x1 <- x[2:n]; x2 <- x[1:(n - 1)]
+     sum(100 * (x1 - x2^2)^2 + (1 - x2)^2)
+ }
> # Equality and inequality constraints
> heq1 <- function(x) sum(x)-1.0
> hin1 <- function(x) -1 * x
> hin2 <- function(x) x - 0.5
> ub <- rep(0.5, n)
> 
> # Apply constraint minimization
> res <- fmincon(x0, fn, hin = hin1, heq = heq1)
Error in fmincon(x0, fn, hin = hin1, heq = heq1) : 
  Package 'NlcOptim' missing -- install from CRAN.
Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'doBy', 'lpSolve', 'plyr', 'pps', 'Rcpp', 'reshape', 'sampling',
  'samplingbook', 'survey', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'PracTools-Ex.R' failed
The error most likely occurred in:

> ### Name: deff
> ### Title: Design effects of various types
> ### Aliases: deff
> ### Keywords: methods survey
> 
> ### ** Examples
> 
> require(reshape)      # has function that allows renaming variables
Loading required package: reshape
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'reshape'
> require(sampling)
Loading required package: sampling
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'sampling'
> 
> set.seed(-500398777)
>     # generate population using HMT function
> pop.dat <- as.data.frame(HMT())
> mos <- pop.dat$x
> pop.dat$prbs.1d <- mos / sum(mos)
>     # select pps sample
> n <- 80
> pk <- n * pop.dat$prbs.1d
> sam <- UPrandomsystematic(pk)
Error in UPrandomsystematic(pk) : 
  could not find function "UPrandomsystematic"
Execution halted
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION 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: 'lmtest', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
TT.test : <anonymous>: no visible global function definition for
  't.test'
TT.test: no visible binding for global variable 'sd'
TT.test: no visible global function definition for 'setNames'
kirjelda : combo: no visible binding for global variable 'sd'
kor.tabel: no visible binding for global variable 'cor.test'
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
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:
  'ROCR', 'PRROC', 'precrec', 'rJava', 'R6', 'assertthat', 'gridExtra',
  'ggplot2', 'memoise'

Packages suggested but not available for checking:
  'microbenchmark', 'PerfMeas', '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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'tibble', 'irr', 'lpSolve', 'purrr',
  'forcats', 'magrittr'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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: 'pbapply', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'devtools', 'ggplot2', 'knitr', 'rmarkdown', 'roxygen2',
  'testthat', '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:
  'magrittr', 'escalation', 'data.table', 'dplyr', 'rlang', 'stringr',
  'knitr', 'kableExtra'

Packages suggested but not available for checking:
  'rmarkdown', 'bookdown', 'tufte', 'testthat', 'latticeExtra',
  'dtpcrm'

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: 'ggplot2', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'magrittr', 'purrr', 'rlang', 'shiny',
  'shinycssloaders', 'shinythemes', 'tidyr'

Packages suggested but not available for checking:
  'ggrepel', 'knitr', 'rmarkdown', 'spelling', 'testthat', 'vdiffr',
  '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: '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:
  'docopt', 'fs', 'here', 'magrittr', 'purrr', 'R.cache', 'rlang',
  'rprojroot', 'rstudioapi', 'usethis', 'withr', 'yaml'

Packages suggested but not available for checking:
  'desc', 'git2r', 'glue', 'knitr', 'lintr', 'reticulate', 'rmarkdown',
  'roxygen2', 'spelling', 'styler', 'testthat', 'versions'

VignetteBuilder 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', 'assertthat', 'gridExtra', 'data.table', 'withr'

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:
  'Biostrings', 'protr', 'Peptides', 'kernlab', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rgl', 'dplyr', 'ggiraphExtra', 'modelr', 'prediction',
  'purrr', 'rlang', 'stringr', 'magrittr', 'moonBook', 'TH.data',
  'reshape2', 'plyr', 'tidyr'

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:
  'Hmisc', 'ROCR', 'PBSmodelling', 'lazyeval'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'MBESS', 'pbapply'

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'

Packages which this enhances but not available for checking:
  'AER', 'aod', 'betareg', 'biglm', 'brglm', 'caret', 'crch', 'e1071',
  'earth', 'ff', 'ffbase', 'gam', 'gee', 'glmnet', 'glmx', 'kernlab',
  'lme4', 'mclogit', 'mda', 'mlogit', 'MNP', 'ordinal', 'plm', 'pscl',
  'quantreg', 'sampleSelection', 'speedglm', 'survey', 'truncreg',
  'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fitdistrplus', 'Renext'

Packages suggested but not available for checking: 'actuar', 'tolerance'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
gausspred: no visible global function definition for 'qt'
mvapred: no visible global function definition for 'qt'
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Packages required but not available:
  'lme4', 'ggplot2', 'numDeriv', 'pbkrtest', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyAce', 'shinydashboardPlus', 'shinyWidgets', 'shinyjs',
  'flexdashboard', 'tidyverse', 'neuralnet', 'rattle', 'xgboost',
  'adabag', 'colourpicker', 'DT', 'randomForest', 'e1071', 'kknn',
  'glmnet', 'ROCR', 'plyr'

Packages suggested but not available for checking:
  'corrplot', 'zip', 'farver'

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', 'testthat', '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:
  'Rcpp', 'maxLik', 'e1071', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

Predict.mix: no visible global function definition for 'dbinom'
abs_cor: no visible global function definition for 'cor'
gen.alpha.IGamma: no visible global function definition for 'qgamma'
gendata.mix: no visible global function definition for 'runif'
gendata.mix: no visible global function definition for 'rbeta'
mh1.unif: no visible global function definition for 'runif'
train_predict_mix: no visible global function definition for 'dbinom'
training: no visible global function definition for 'runif'
training: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Packages required but not available:
  'plyr', 'ggplot2', 'caret', 'e1071', 'mclust', 'party',
  'randomForest', 'statmod'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'rpart'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'caret', 'forecast', 'Metrics', 'TSPred', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pkgdown', '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', '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: 'mcmc', 'entropy'

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: 'gnm', 'colorspace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'plotrix', 'gamlss.dist', 'data.table', 'spdep',
  'rgdal', 'RcppEigen', '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: 'dplyr', 'reshape2', 'psych'

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: 'plotrix', 'shape'

Packages suggested but not available for checking:
  'bookdown', 'knitr', 'rmarkdown', 'ggplot2', 'gridBase'

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: 'oompaBase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'psycho', 'dplyr'

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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'earth', 'Formula', 'glmnet', 'partykit', 'stringr', 'MatrixModels'

Packages suggested but not available for checking:
  'akima', 'doParallel', 'foreach', 'glmertree', 'mlbench', 'testthat',
  'mboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rmarkdown'

Package suggested but not available for checking: 'testthat'

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: 'marelac', 'measurements'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'
Note: found 42966 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: 'polynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'rms', 'SparseM'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'kappaSize', 'shiny'

Packages suggested but not available for checking:
  'binom', 'ggplot2', 'Hmisc', 'testthat', 'shinydashboard',
  'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survPresmooth'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'callr', 'curl', 'glue', 'jsonlite', 'testthat', 'withr'
Packages unavailable to check Rd xrefs: 'jsonlite', 'callr', 'glue'
'LazyData' is specified without a 'data' directory
Running examples in 'presser-Ex.R' failed
The error most likely occurred in:

> ### Name: httpbin_app
> ### Title: Generic web app for testing HTTP clients
> ### Aliases: httpbin_app
> 
> ### ** Examples
> 
> app <- httpbin_app()
> proc <- new_app_process(app)
Error in loadNamespace(x) : there is no package called 'callr'
Calls: new_app_process ... 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:
  'data.table', 'ggplot2', 'gridExtra', 'reticulate'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp', 'qpdf'

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:
  'shiny', 'rstudioapi', 'xml2', 'webdriver', 'XRJulia', 'httr'

Packages suggested but not available for checking:
  'V8', 'shinythemes', 'shinyAce', 'miniUI', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'knitr', 'lintr', 'rmarkdown', 'testthat', 'vdiffr'

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: 'crayon'

Packages suggested but not available for checking:
  'covr', 'mockery', 'rstudioapi', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rmarkdown'

Package suggested but not available for checking: 'knitr'

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: 'digest', 'rjson', 'httr', 'plyr'

Packages suggested but not available for checking:
  'maptools', 'raster', 'rosm', 'testthat', 'rgdal', 'sp'

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: 'rjags', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maxLik', 'raster', 'pdist', 'splancs', 'lme4', 'truncnorm',
  'numDeriv'

Packages suggested but not available for checking:
  'geoR', 'R.rsp', 'INLA', 'knitr', '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:
  'sp', 'rgdal', 'ggplot2', 'directlabels', 'GenKern', 'fields',
  'gstat', 'maptools'

Packages suggested but not available for checking:
  'geoR', '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', 'rlang', 'tibble', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'gridExtra', '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:
  'ape', 'future', 'future.apply', 'phangorn', 'vcfR'

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', 'permute', 'randomForest', 'reshape2', 'dplyr', 'multtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'ggplot2', 'reshape', 'reclin', 'stringr',
  'xgboost', 'caret', 'strex'

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', 'gsubfn', 'stringr', 'purrr', 'jsonlite', 'lubridate',
  'curl', '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: 'survey', 'ggplot2', '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: 'Rcpp', 'RcppEigen'

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
Package required but not available: 'softImpute'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'deSolve', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'bbmle', 'bipartite', 'cowplot', 'data.table', 'diagram',
  'DiagrammeR', 'DiagrammeRsvg', 'gdata', 'igraph', 'lavaan',
  'magrittr', 'phaseR', 'vegan', 'reshape2', 'rARPACK', 'rsvg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'directlabels', 'gridExtra', 'ggplot2', 'XML', 'ape', 'httr',
  'lubridate', 'plyr', 'scales', 'stringr', 'foreach', 'reshape2',
  'RCurl'

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.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'scales', 'plot3D'

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: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
basisplot: no visible global function definition for 'abline'
basisplot: no visible global function definition for 'text'
basisplot: no visible global function definition for 'par'
plot.prinsimp: no visible global function definition for 'screeplot'
plot.simpart: no visible global function definition for 'par'
position_text: no visible global function definition for 'par'
position_text: no visible global function definition for 'strwidth'
simpart.formula: no visible global function definition for 'terms'
simpart.formula: no visible global function definition for
  'model.matrix'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'points'
varsimp: no visible global function definition for 'text'
varsimp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines model.matrix par points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
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: 'AnnotationDbi', 'org.Hs.eg.db'

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', 'ROCR', 'visNetwork'

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: 'rootSolve'

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:
  'testthat', 'roxygen2', 'knitr', 'rgeos', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'sp', 'sf', 'proto', 'assertthat', 'data.table', 'uuid',
  'slam', 'igraph', 'ape', 'rgeos', 'plyr', 'doParallel', 'magrittr',
  'exactextractr', 'fasterize', 'tibble', 'withr', 'Rcpp',
  'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'roxygen2', 'scales', 'xtable', 'RandomFields',
  'maptools', 'PBSmapping', 'gurobi', 'rcbc', 'cplexAPI', 'lpsymphony',
  'Rsymphony', 'rmarkdown', 'prioritizrdata'

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: 'glmnet'

Packages suggested but not available for checking:
  'testthat', '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: 'dplyr', 'DiagrammeR'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'flextable'

VignetteBuilder 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', 'ggplot2'

Package suggested but not available for checking: 'tm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DiagrammeR'

Packages suggested but not available for checking:
  'DiagrammeRsvg', 'knitr', 'rmarkdown', 'rsvg', 'scales', '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: 'farver'

Packages suggested but not available for checking:
  'covr', 'crayon', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'glmnet', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'raster', 'httr', 'dplyr', 'stringr',
  'magrittr', 'purrr', 'readr'

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:
  'sf', 'dplyr', 'httr', 'magrittr', 'passport', 'rnaturalearth',
  'rnaturalearthdata', 'rvest', 'stringr', 'tibble', 'tidyr', 'xml2'

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', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggnewscale', 'ggtext', 'dplyr', 'Hmisc', 'magrittr',
  'ExactCIdiff', 'DescTools'

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', 'generics', 'rlang', 'tidyselect', 'vctrs', 'yardstick'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'modeldata', 'parsnip', 'rmarkdown',
  'rsample', '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:
  'LearnBayes', 'ggplot2', 'gridExtra', 'shiny'

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: 'TmCalculator', 'Biostrings'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.pfda.fstep: no visible global function definition for 'dist'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist
Consider adding
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
Packages required but not available: 'barsurf', 'kubik'

Packages suggested but not available for checking:
  'bivariate', 'fclust', 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FNN', 'mclust'

Packages suggested but not available for checking:
  'mvtnorm', 'GDAdata', 'bibtex', '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: 'combinat', 'fAsianOptions'

Packages suggested but not available for checking:
  'VGAM', 'reshape', 'hypergeo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'purrr', 'mvtnorm', 'Rdpack', 'RcppEigen', 'StanHeaders',
  'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'fable', 'dplyr', 'tidyr', 'magrittr',
  '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:
  'shiny', 'rmarkdown', 'LaplacesDemon', 'shinyMatrix', 'rpivotTable',
  'epitools'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'keras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'codemetar'
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:
  'bupaR', 'processmapR', 'rlang', 'magrittr', 'dplyr', 'tidyr',
  'htmlwidgets', 'DiagrammeR', 'stringr', 'htmltools'

Packages suggested but not available for checking:
  'eventdataR', 'edeaR', 'testthat', 'knitr', 'rmarkdown', 'shiny',
  'RColorBrewer', 'lubridate'

VignetteBuilder 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', 'bupaR', 'rlang', 'edeaR', 'stringr', 'glue'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'eventdataR'

VignetteBuilder 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', 'bupaR', 'edeaR', 'DiagrammeR', 'ggplot2', 'ggthemes',
  'stringr', 'purrr', 'data.table', 'shiny', 'miniUI', 'glue',
  'forcats', 'hms', 'RColorBrewer', 'plotly', 'rlang', 'scales',
  'tidyr', 'htmltools', 'Rcpp', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'eventdataR'

VignetteBuilder 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', 'ggplot2', 'dplyr', 'bupaR', 'edeaR', 'shiny', '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:
  'lavaan', 'diagram', 'dplyr', 'flextable', 'ggplot2', 'ggrepel',
  'officer', 'psych', 'purrr', 'rrtable', 'semTools', 'stringr',
  'tidyselect', 'rlang', 'tidyr', 'predict3d', 'interactions',
  'ztable', 'rmarkdown'

Packages suggested but not available for checking:
  'shiny', 'shinyWidgets', 'knitr', 'readr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ps', 'R6'

Packages suggested but not available for checking:
  'callr', 'cli', 'covr', 'curl', 'debugme', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'testthat', 'tibble'
Package unavailable to check Rd xrefs: 'tibble'
'LazyData' is specified without a 'data' directory
Running 'output.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: 'plyr', 'Rcpp'

Packages suggested but not available for checking:
  'microbenchmark', 'logcondens', 'doParallel', 'testthat', 'vdiffr',
  'ggplot2'

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: 'dplyr', 'Rsolnp', 'DEoptim', 'AER'

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', 'git2r', 'rmarkdown', 'rprojroot', 'usethis', 'withr'

Packages suggested but not available for checking:
  'devtools', 'covr', '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: 'Rcpp', 'lava'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lpSolveAPI', 'doParallel', 'foreach', 'iterators'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'ggplot2'

Packages suggested but not available for checking:
  'reshape2', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RPMG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DiceKriging', 'KrigInv', 'pGPx', 'microbenchmark', 'quantreg',
  'lhs', 'RColorBrewer', 'rcdd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'pingr', 'processx', 'profile', 'RProtoBuf', 'withr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'MASS' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'gnm'
Packages required but not available: 'rlang', 'tibble', 'withr'

Packages suggested but not available for checking:
  'dm', 'DiagrammeR', 'DiagrammeRsvg', 'RProtoBuf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'RColorBrewer', 'reshape', 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FITSio', 'magicaxis', 'cubature', 'RColorBrewer', 'LaplacesDemon',
  'celestial', 'checkmate'

Packages suggested but not available for checking:
  'fftw', 'knitr', 'rmarkdown', 'ProFound', 'sn'

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:
  'R.rsp', 'markdown', 'microbenchmark'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Packages required but not available:
  'sqldf', 'DBI', 'RSQLite', 'RNetCDF', 'settings', 'zoo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp', 'testthat', 'BayesianTools'

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:
  'FITSio', 'magicaxis', 'Rcpp', 'RColorBrewer', 'data.table',
  'celestial', 'foreach'

Packages suggested but not available for checking:
  'ProFit', 'knitr', 'rmarkdown', 'EBImage', 'imager', 'LaplacesDemon',
  'Rfast', 'fastmatch', 'snow', 'doSNOW', 'bigmemory'

VignetteBuilder 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'

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:
  'graph', 'Rgraphviz', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/proftools.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/proftools.Rnw'
(Is a VignetteBuilder field missing?)
Running examples in 'proftools-Ex.R' failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(x) : there is no package called 'graph'
Calls: plotProfileCallGraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'data.tree'

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: 'htmlwidgets', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'rmarkdown', 'testthat', 'devtools', 'shiny',
  'htmltools'

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 in Depends field not imported from:
  'splines' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for 'survfit'
IndividualPROC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Packages required but not available: 'hms', 'prettyunits', 'R6', 'crayon'

Packages suggested but not available for checking:
  'Rcpp', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'digest'

Packages suggested but not available for checking:
  'beepr', 'crayon', 'pbmcapply', 'progress', 'purrr', 'foreach',
  'plyr', 'doFuture', 'future', 'future.apply', 'furrr', 'shiny',
  'commonmark', 'base64enc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'vegan', 'deldir', 'geometry',
  'GeneralizedUmatrix', 'shiny', 'shinyjs', 'shinythemes', 'plotly'

Packages suggested but not available for checking:
  'DataVisualizations', 'fastICA', 'tsne', 'FastKNN', 'pcaPP', 'spdep',
  'pracma', 'fields', 'png', 'reshape2', 'Rtsne', 'dendextend', 'umap',
  'uwot', 'DatabionicSwarm', 'parallelDist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'incidence', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown', 'outbreaks',
  'magrittr', 'distcrete', 'svglite', 'EpiEstim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotly', 'GameTheory', 'lpSolveAPI', 'triangle', 'kappalab',
  'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fs', 'lubridate', 'magrittr', 'purrr', 'readr', 'rlang',
  'rstudioapi', 'sessioninfo', 'stringr', 'tibble', 'vctrs', 'zip'

Packages suggested but not available for checking:
  'forcats', 'here', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'feather', 'reshape', 'plyr', 'digest', 'formatR', 'qs', 'stringr',
  'ggplot2', 'lubridate', 'log4r', 'DBI', 'RMySQL', 'RSQLite', 'gdata',
  'RODBC', 'RJDBC', 'readxl', 'xlsx', 'tuneR', 'pixmap', 'data.table',
  'RPostgreSQL', 'GetoptLong', 'whisker', 'tibble', 'testthat'
Package unavailable to check Rd xrefs: 'qs'
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: 'gh', 'magrittr'

Packages suggested but not available for checking:
  'clipr', 'curl', 'dplyr', 'ggplot2', 'knitr', 'purrr', 'reprex',
  'rmarkdown', 'testthat', 'tidyr', 'yaml', 'htmltools', 'httr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'loo', 'rstantools', 'lme4', 'optimx', 'ggplot2', 'Rcpp',
  'rngtools', 'tidyverse', 'magrittr', 'gamm4', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rstanarm', 'brms', 'testthat', 'knitr', 'rmarkdown', 'glmnet',
  'bayesplot'

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', 'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpSolve'

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:
  'R6', 'Rcpp', 'later', 'rlang', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'future', 'fastmap', 'purrr', 'knitr', 'rmarkdown',
  'vembedr', '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: 'httr', 'jsonlite', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'ggplot2', 'scales', 'ggpubr', 'reshape2',
  'stringr', 'strucchange', 'lmtest', 'crayon', 'prophet'

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.
Package required but not available: 'cli'

Packages suggested but not available for checking:
  'callr', 'gert', 'mockery', 'pkgload', 'ps', 'R6', 'rstudioapi',
  'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tmvtnorm', 'Rcpp', 'ff', 'minpack.lm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fastcluster', 'dynamicTreeCut'

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:
  'Rcpp', 'rlang', 'dplyr', 'dygraphs', 'extraDistr', 'ggplot2',
  'lubridate', 'RcppParallel', 'rstan', 'rstantools', 'scales',
  'StanHeaders', 'tidyr', 'xts', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'readr', '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: 'TeachingDemos', 'ggplot2'

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: 'Biobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fastcluster', 'ggplot2', 'igraph', 'Rcpp'

Packages suggested but not available for checking:
  'ALDEx2', 'Biobase', 'cccrm', 'compositions', 'data.table',
  'ggdendro', 'knitr', 'limma', 'plotly', 'reshape2', 'rgl',
  'rmarkdown', 'SDMTools', 'testthat', 'vegan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
addpi: no visible global function definition for 'lines'
genPerms: no visible global function definition for 'combn'
getVar: no visible global function definition for 'glm'
getVar: no visible global function definition for 'binomial'
getVar: no visible global function definition for 'var'
pba: no visible global function definition for 'glm'
pba: no visible global function definition for 'binomial'
pba: no visible global function definition for 'predict'
pba: no visible global function definition for 'rbinom'
pcr: no visible global function definition for 'quantile'
plotpi: no visible global function definition for 'axis'
plotpi: no visible global function definition for 'abline'
plotpi: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline axis binomial combn glm lines predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available: 'httr', 'dplyr', '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:
  'dplyr', 'stringr', 'httr', 'config', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'httptest', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'cin'
Packages required but not available:
  'fmsb', 'car', 'RColorBrewer', 'matrixcalc', 'rootSolve', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'PROscorerTools'

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.
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
Packages required but not available:
  'equate', 'lavaan', 'mirt', 'plink', 'psych', 'mvnfast'

Packages suggested but not available for checking:
  'shiny', 'shinythemes', 'shinyWidgets', 'shinyjs', 'DT', 'knitr',
  'kableExtra', 'testthat', 'rmarkdown', 'dplyr', 'pkgdown'

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: 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'iterators', 'Rcpp', 'mathjaxr', 'lifecycle',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'formatR', 'testthat', 'bookdown'

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: 'ggplot2', 'dplyr', 'RColorBrewer'

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
Package in Depends field not imported from: 'MASS'
  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:
  'plyr', 'reshape2', 'ggplot2', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'class' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'class'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'box'
plot.protoclass: no visible global function definition for 'rgb2hsv'
plot.protoclass: no visible global function definition for 'col2rgb'
plot.protoclass: no visible global function definition for 'points'
plot.protoclass: no visible global function definition for 'hsv'
predict.protoclass: no visible global function definition for 'knn1'
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "points")
to your NAMESPACE file.
Extract_plant_grapevine_function: no visible global function definition
  for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'jsonlite'

Packages suggested but not available for checking:
  'spelling', 'curl', 'testthat', 'RProtoBuf', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'digest'

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:
  'intervals', 'glmnet', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'audio', 'signal', 'tuneR', 'XML'

Package suggested but not available for checking: 'AmigaFFH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Biostrings', 'GOSemSim', 'foreach',
  'doParallel', 'org.Hs.eg.db'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'rlang', 'dplyr', 'stringr', 'magrittr', 'data.table', 'janitor',
  'progress', 'purrr', 'tidyr', 'ggplot2', 'forcats', 'tibble',
  'plotly', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'proDA', 'limma',
  'dendextend', 'pheatmap', 'heatmaply', 'viridis', 'iq', 'furrr',
  'future', 'seriation', 'drc', 'naniar', 'httr', 'igraph', 'stringi',
  'STRINGdb'

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', 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'rlang', 'tidyr', 'tokenizers', 'SnowballC', 'attempt'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', '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:
  'httr', 'jsonlite', 'provGraphR', 'provParseR', 'textutils'

Packages suggested but not available for checking:
  'knitr', 'rdtLite', 'rdt', '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: 'IsoplotR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'provParseR', 'diffobj', 'digest', '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: 'igraph', 'provParseR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: '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: 'dplyr', 'provParseR'

Packages suggested but not available for checking:
  'rdtLite', 'rdt', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'provParseR'

Packages suggested but not available for checking:
  'digest', 'knitr', 'rdt', 'rdtLite', '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: 'rdt', 'rdtLite'
Packages required but not available:
  'Rcpp', 'RcppParallel', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'proxy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'cba'
Running 'apply.R'
  Comparing 'apply.Rout' to 'apply.Rout.save' ... OK
  Running 'distance.R'
  Comparing 'distance.Rout' to 'distance.Rout.save' ... OK
  Running 'distcalls.R'
Running the tests in 'tests/distcalls.R' failed.
Last 13 lines of output:
  > for (j in c(0.5, 1, 2, 3, Inf))
  +     {cat("Minkowski: p =", j); prtest("Minkowski", p = j); cat(": OK.\n")}
  Minkowski: p = 0.5: OK.
  Minkowski: p = 1: OK.
  Minkowski: p = 2: OK.
  Minkowski: p = 3: OK.
  Minkowski: p = Inf: OK.
  > 
  > ## Levenshtein distance
  > s <- c("A", "quick", "brown", "fox", "jumps", "over", "the", "lazy", "dog")
  > all(as.matrix(dist(s, "Levenshtein")) == dist(s, s, "Levenshtein"))
  Error in pr_Levenshtein_prefun(c("A", "quick", "brown", "fox", "jumps",  : 
    Need package 'cba'!
  Calls: as.matrix ... <Anonymous> -> dist -> do.call -> pr_Levenshtein_prefun
  Execution halted
Packages required but not available:
  'AhoCorasickTrie', 'doParallel', 'foreach', 'plyr', 'readr',
  'seqinr', 'stringr', '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:
  'config', 'liteq', 'data.table', 'crayon', 'DBI', 'RSQLite'

Packages suggested but not available for checking: 'docopt', 'foghorn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ROCR'
Running 'all_tests.R'
Running the tests in 'tests/all_tests.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Errors in running code in vignettes:
when running code in 'PRROC.Rnw'
  ...
+     ylab = "Precision", t = "l")

> plot(curve.points[, 1], curve.points[, 2], xlab = "Recall", 
+     ylab = "Precision", t = "l")

> library(ggplot2)

  When sourcing 'PRROC.R':
Error: there is no package called 'ggplot2'
Execution halted

  'PRROC.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'PRROC.Rnw' using Sweave

Error: processing vignette 'PRROC.Rnw' failed with diagnostics:
 chunk 47 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'PRROC.Rnw'

SUMMARY: processing the following file failed:
  'PRROC.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'homtest', 'goftest', 'wavScalogram', 'splus2R', 'lmomco', 'mev'

Packages suggested but not available for checking: 'ismev', 'evd', 'GB2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'fst', 'data.table', 'vctrs', 'tibble', 'cli',
  'pillar', 'crayon', 'fansi', 'backports', 'rlang', 'knitr'

Packages suggested but not available for checking:
  'testthat', 'xml2', 'covr', 'withr', 'nycflights13', 'rmarkdown',
  'bench'

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: 'Morpho'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'geomorph'

VignetteBuilder 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', '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: 'PogromcyDanych', 'PBImisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'rpart'
  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: 'LearnBayes', 'SuppDists', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.methodsS3', 'R.oo', 'R.utils', 'R.cache', 'matrixStats',
  'aroma.light', 'DNAcopy', 'listenv', 'future'

Packages suggested but not available for checking:
  'Hmisc', 'R.rsp', 'R.devices', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'MCMCpack', 'car', 'lmtest', 'sandwich', 'zoo', 'coda', 'vcd',
  'mvtnorm'
Packages unavailable to check Rd xrefs: 'car', 'MCMCpack', 'coda'
Running examples in 'pscl-Ex.R' failed
The error most likely occurred in:

> ### Name: UKHouseOfCommons
> ### Title: 1992 United Kingdom electoral returns
> ### Aliases: UKHouseOfCommons
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(UKHouseOfCommons)
> tmp <- UKHouseOfCommons[,c("v1","v2","v3")] 
> summary(apply(tmp,1,sum))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.9999  1.0000  1.0000  1.0000  1.0000  1.0001 
> 
> col <- rep("black",dim(tmp)[1])
> col[UKHouseOfCommons$coninc==1] <- "blue"
> col[UKHouseOfCommons$labinc==1] <- "red"
> col[UKHouseOfCommons$libinc==1] <- "orange"
> 
> library(vcd)
Error in library(vcd) : there is no package called 'vcd'
Execution halted
Errors in running code in vignettes:
when running code in 'countreg.Rnw'
  ...

> library("sandwich")

  When sourcing 'countreg.R':
Error: there is no package called 'sandwich'
Execution halted

  'countreg.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'countreg.Rnw' using Sweave

Error: processing vignette 'countreg.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("sandwich") : there is no package called 'sandwich'

--- failed re-building 'countreg.Rnw'

SUMMARY: processing the following file failed:
  'countreg.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'reshape2', 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rgeos', 'plyr', 'sp', 'raster'

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:
  'countrycode', 'DataCombine', 'reshape2', 'rio', 'xlsx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RColorBrewer', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bspec', 'fftw', 'ggplot2', 'multitaper', 'plyr', 'RSEIS',
  'rbenchmark', 'reshape2', 'knitr', 'rmarkdown', 'signal', 'formatR',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/fftw.Rnw'
   'inst/doc/multivariate.Rnw'
   'inst/doc/normalization.Rnw'
   'inst/doc/psd_overview.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

Packages suggested but not available for checking: 'sensitivity', 'mcmc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'doBy'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'KMsurv', 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'knitr', 'printr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'simulation-study.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'norm', 'mitools', 'pROC', 'rms', 'ResourceSelection',
  'magrittr', 'rsample', 'mice', 'mitml', 'cvAUC', 'dplyr', 'purrr',
  'tidyr', 'tibble', 'stringr', 'lme4', 'miceadds', 'car'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'bookdown', 'readr'

VignetteBuilder 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', 'knitr', 'forecast'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'intamap', 'gstat', 'automap', 'sp', 'doParallel', 'rgdal',
  'foreach', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'gridBase', 'randomForest', 'partykit', 'party',
  'BayesTree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'RCurl', 'SAScii', 'openxlsx', 'futile.logger'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MCMCglmm', 'plotrix', 'pedigree', 'knitr'

Packages suggested but not available for checking: 'AICcmodavg', 'psych'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/PSIMEXvignette.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'numDeriv'
'library' or 'require' call to 'numDeriv' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' 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.
test.problem : g: no visible global function definition for 'grad'
test.problem: no visible global function definition for 'new'
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for 'new'
show,test.result: no visible global function definition for 'show'
show,test.result: no visible global function definition for 'sd'
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
pspearman: no visible global function definition for 'pt'
spearman.test: no visible global function definition for
  'complete.cases'
spearman.test: no visible global function definition for 'cor'
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'magrittr', 'assertthat', 'plyr', 'reshape2', 'plotrix',
  'rlang'

Packages suggested but not available for checking:
  'import', 'ggplot2', 'data.table', 'ggstance', 'knitr', 'rmarkdown',
  'roxygen2', 'kableExtra', 'doParallel', 'stringr', '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: 'rstudioapi', 'pkgbuild'

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.
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Packages suggested but not available for checking:
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  'testthat', 'numDeriv', 'lbfgsb3c', 'lbfgs'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'testthat', 'tibble'
Packages unavailable to check Rd xrefs: 'testthat', 'processx'
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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  'RcppEigen', 'StanHeaders'

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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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  'kappaSize', 'longpower', 'plotly', 'powerMediation', 'powerSurvEpi',
  'presize', 'pROC', 'pwr', 'pwr2', 'shiny', 'shinycssloaders',
  'shinyFeedback', 'shinyhelper', 'tidyverse', 'writexl'

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: 'osDesign', 'np', 'chngpt'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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: '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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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: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'reshape2', 'ggplot2', 'metafor', 'progress',
  'tidyr', 'stringi', 'stringr', 'rlang', 'curl', 'purrr', 'data.table'

Packages suggested but not available for checking:
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  'knitr', '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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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:
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  'glasso', 'optimx', 'VCA', 'pbapply', 'magrittr', 'IsingSampler',
  'tidyr', 'psych', 'GA', 'combinat', 'Rcpp', 'RcppArmadillo', 'pbv',
  'roptim'

Packages suggested but not available for checking:
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  'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'parameters', 'effectsize'

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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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/scoring.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cli', 'dplyr', 'ez', 'xtable'

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: 'testthat', 'covr'

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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  'lmerTest', 'parameters', 'performance', 'psych', 'rlang', 'stringr',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
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  'gridExtra', 'interactions', 'knitr', 'nFactors', 'pagedown',
  'qqplotr', 'rmarkdown', 'roxygen2', 'sandwich', 'see', 'semPlot',
  'testthat', 'tidyselect'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ltm', 'irtoys'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doParallel', 'foreach', 'magrittr'

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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  'RgoogleMaps', 'Hmisc'

Package suggested but not available for checking: 'ggmap'

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: 'yaml', 'yum'

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: 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quantreg'

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: 'rgl', 'geometry'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'numDeriv', 'tweeDEseq'

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', 'Biostrings', 'httr', 'igraph', 'jsonlite', 'muscle',
  'RCurl', 'seqinr', 'xml2', 'XML'

Packages suggested but not available for checking:
  'KEGGREST', 'knitr', 'markdown', 'rmarkdown', 'stringr', '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:
  'this.path', 'log4r', 'beepr', 'pryr', 'stringi', 'stringr'

Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'plotly'

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', 'dplyr', 'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required but not available: 'nloptr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'ggplot2', 'ggdendro', 'gtable', 'jsonlite',
  'kableExtra', 'knitr', 'ontologyIndex', 'plyr', 'RColorBrewer',
  'reshape2', 'rmarkdown', 'seqinr', 'UpSetR', 'yaml'

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', 'plyr', 'reshape2'

Packages suggested but not available for checking: 'foreach', 'doRNG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rmeta', 'R.utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xml2', 'data.table', 'rcrossref'

Packages suggested but not available for checking: 'fulltext', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'emmeans', 'ggformula', 'magrittr', 'car', 'dplyr', 'Epi', 'epiR',
  'epitools', 'ggplot2', 'Hmisc', 'huxtable', 'lmtest', 'moonBook',
  'sandwich', 'sjlabelled', 'sjmisc', 'sjPlot', 'tibble', 'tidyselect'

Packages suggested but not available for checking:
  'broom', 'bookdown', 'GGally', 'ggeffects', 'ggfortify', 'ggpubr',
  'ggsci', 'haven', 'ISwR', 'jtools', 'knitr', 'latex2exp', 'lme4',
  'mosaic', 'performance', 'psych', 'reshape2', 'rmarkdown', 'rms',
  'scales', '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:
  'metafor', 'dplyr', 'robumeta', 'ggplot2', 'Rdpack', 'MetaUtility'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'loo', 'truncnorm', 'BH', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'metafor', 'qtl',
  'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'prodlim', 'data.table', 'lava', 'multcomp'

Packages suggested but not available for checking:
  'riskRegression', 'testthat', 'smcfcs', 'rms', 'mitools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', 'XML', 'R2HTML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'easyPubMed', '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: 'rentrez', '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.
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:
  'DBI', 'R.utils', 'RSQLite', 'assertthat', 'dplyr', 'readr'

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:
  'Rcpp', 'doParallel', 'foreach', 'ggplot2', '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: 'RCurl'

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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  'network', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'batchtools'
Running examples in 'pulsar-Ex.R' failed
The error most likely occurred in:

> ### Name: findConfFile
> ### Title: find config file
> ### Aliases: findConfFile
> 
> ### ** Examples
> 
> ## Default config file provided by pulsar runs code in interactive mode
> ## This is for testing purposes and executes serially.
> findConfFile()
Error in loadNamespace(x) : there is no package called 'batchtools'
Calls: findConfFile ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > suppressPackageStartupMessages(library(testthat))
  Error in library(testthat) : there is no package called 'testthat'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Packages required but not available:
  'AnnotationDbi', 'SummarizedExperiment', 'Rsamtools', 'Biobase',
  'S4Vectors', 'GenomicFeatures', 'ggplot2', 'GenomicAlignments'

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:
  'dplyr', 'fda', 'fda.usc', 'ggplot2', 'monoClust', 'purrr', 'rlang',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'knitr', 'lubridate', 'rmarkdown', '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: 'XML', 'RCurl'

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', 'ADGofTest', 'metafor', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nls2', 'Metrics', 'minpack.lm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rlang', 'data.table', 'fda', 'itsadug',
  'lazyeval', 'signal', 'tidyr', '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:
  'dplyr', 'rlang', 'VWPre', 'ggplot2', 'shiny', 'tidyr', 'robustbase',
  'zoo', 'signal'

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: 'rjags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'rappdirs', 'stringr', '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 suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
Running 'purged.filesizes.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
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'magrittr', 'purrr', 'Rcpp', 'BH'

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: 'magrittr', 'rlang'

Packages suggested but not available for checking:
  'covr', 'crayon', 'dplyr', 'knitr', 'rmarkdown', 'testthat',
  'tibble', 'tidyselect'

VignetteBuilder 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', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lubridate', 'readxl', 'reshape', 'reshape2', 'sqldf', 'kableExtra',
  'plyr', 'dplyr', 'tidyverse', 'readr'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dcmle', 'dclone', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'scales', 'zipfR', 'pracma'

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.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'e1071', 'testthat', 'knitr', 'formatR'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/pvar_intro.Rnw'
(Is a VignetteBuilder field missing?)

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', 'broom', 'ggplot2', 'stlplus', 'purrr', 'tidyr',
  'minpack.lm', 'rlang', 'segmented'

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: 'splancs', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'httr'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'maps', 'MazamaCoreUtils', 'MazamaSpatialUtils', 'curl',
  'dygraphs', 'geosphere', 'ggmap', 'glue', 'httr', 'jsonlite',
  'leaflet', 'lubridate', 'magrittr', 'mapproj', 'maptools', 'openair',
  'png', 'purrr', 'raster', 'RColorBrewer', 'rgdal', 'RgoogleMaps',
  'readr', 'reshape2', 'rlang', 'sf', 'slippymath', 'sp', 'stringr',
  'tibble', 'tidyr', 'xts'

Packages suggested but not available for checking:
  'knitr', '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:
  'car', 'dplyr', 'tidyr', 'ez', 'phia', 'afex', 'MBESS', 'lavaan'

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 suggested but not available for checking:
  'eRm', 'roxygen2', 'testthat'
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'scales', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
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: 'httr', 'rjstat', 'jsonlite', 'pxweb'

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: 'checkmate', 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'remotes', '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: 'sp', 'maptools', 'rgeos'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'robustbase'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'knitr', 'reticulate', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', '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: 'xml2'

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
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 required but not available:
  'ggplot2', 'data.table', 'copula', 'viridis', 'ggExtra', 'dplyr',
  'cowplot', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', '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.
Packages required but not available: 'lme4', 'mvtnorm', 'plyr', 'dplyr'

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:
  'ncdf4', 'gplots', 'XML', 'gdata', 'moments', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ald', 'zipfR', 'GoFKernel', 'Deriv', 'nloptr', 'quantreg', 'locpol',
  'scdensity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'mcmcse', 'stableGR', 'RcppDist', 'knitr', 'rmarkdown',
  'RcppArmadillo'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/qbld.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
csQCAbinTest: no visible global function definition for 'p.adjust'
fsQCApermTest: no visible global function definition for 'p.adjust'
mvQCAbinTest: no visible global function definition for 'p.adjust'
p.threshold.adjust: no visible global function definition for
  'p.adjust'
plot.fsQCApt: no visible global function definition for 'dev.cur'
plot.fsQCApt: no visible global function definition for 'dev.new'
plot.fsQCApt: no visible global function definition for 'par'
plot.fsQCApt: no visible global function definition for 'density'
plot.fsQCApt: no visible global function definition for 'axis'
plot.fsQCApt: no visible global function definition for 'polygon'
plot.fsQCApt: no visible global function definition for 'points'
plot.fsQCApt: no visible global function definition for 'hist'
summary.csQCAbt: no visible global function definition for
  'printCoefmat'
summary.fsQCApt: no visible global function definition for
  'printCoefmat'
summary.mvQCAbt: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "points", "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'ggforce', '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: 'lpSolve'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'admisc', 'shiny', 'venn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'ggplot2', 'directlabels', 'QCA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arules', 'rJava', 'arc'

Packages suggested but not available for checking:
  'arulesCBA', 'rCBA', 'stringr'

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: 'dplyr', 'magrittr', 'purrr', 'tibble'

Package suggested but not available for checking: 'testthat'

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: 'ggplot2'

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 unavailable to check Rd xrefs: 'qdap'
Packages required but not available:
  'qdapDictionaries', 'qdapRegex', 'qdapTools', 'RColorBrewer',
  'chron', 'dplyr', 'gender', 'ggplot2', 'gridExtra', 'igraph', 'NLP',
  'openNLP', 'openxlsx', 'plotrix', 'RCurl', 'reshape2', 'scales',
  'stringdist', 'tidyr', 'tm', 'venneuler', 'wordcloud', 'XML'

Packages suggested but not available for checking:
  'koRpus', 'knitr', 'lda', 'proxy', 'stringi', 'SnowballC', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: '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: 'chron', 'data.table', 'RCurl', 'XML'

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: 'tinytest'
Packages required but not available:
  'Rsolnp', 'futile.logger', 'gamlss', 'gamlss.dist'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'plyr', 'gtools'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rsolnp'

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', 'RcppGSL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'RColorBrewer', 'R.utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'plyr', 'doParallel'

Packages suggested but not available for checking:
  'knitr', 'RhpcBLASctl', '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', 'robustbase', 'zipfR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'arm', 'future', 'future.apply', 'generics', 'ggplot2', 'gridExtra',
  'pscl', 'tibble'

Packages suggested but not available for checking:
  'broom', 'devtools', 'knitr', 'markdown', 'mice'

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.
Packages required but not available: 'data.table', 'statmod', 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'psych', 'lavaan', 'plyr', 'Hmisc', 'igraph', 'jpeg', 'png',
  'colorspace', 'corpcor', 'reshape2', 'ggplot2', 'glasso', 'fdrtool',
  'gtools', 'pbapply', 'abind', 'dplyr'

Packages suggested but not available for checking: 'BDgraph', 'huge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'FactoClass', 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'dplyr', '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: 'latticeExtra', 'scales', '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:
  'httr', 'jsonlite', 'purrr', 'rstudioapi'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'QKPIs-Ex.R' failed
The error most likely occurred in:

> ### Name: QKPIs-package
> ### Title: Quantitative Key Performance Indicators
> ### Aliases: QKPIs-package QKPIs
> 
> ### ** Examples
> 
> ## For Sales metric
> df1 = data.frame(jan =c(23455, 56432, 64344), Feb = c(21145, 43213, 76433), Mar = c(2355, 
+ 86432, 64344), April= c(41149, 67746, 43203), May= c(85438, 05847,6849), 
+ June = c(5565,44253, 78253))
> sam(status = df1, tgoal = 54635, dtev = 1)
Error in assign("snm", c(NULL), envir = .BaseNamespaceEnv) : 
  cannot add binding of 'snm' to the base environment
Calls: sam -> assign
Execution halted
Packages required but not available: 'slam', 'sparsesvd', 'docopt'

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.
'LazyData' is specified without a 'data' directory
chooseMDoubleBootstrap: no visible global function definition for
  'model.matrix'
chooseMDoubleBootstrap: no visible global function definition for
  'as.formula'
chooseMDoubleBootstrap: no visible global function definition for
  'model.frame'
chooseMDoubleBootstrap: no visible global function definition for 'lm'
chooseMDoubleBootstrap: no visible global function definition for
  'coef'
chooseMDoubleBootstrap: no visible global function definition for
  'quantile'
chooseMDoubleBootstrap: no visible global function definition for
  'qnorm'
getModel: no visible global function definition for 'lm'
getModel: no visible global function definition for 'model.matrix'
getModel: no visible global function definition for 'as.formula'
getModel: no visible global function definition for 'model.frame'
getModel: no visible global function definition for 'model.response'
getModel: no visible global function definition for 'coef'
getModel: no visible global function definition for 'qnorm'
qLearn: no visible global function definition for 'model.matrix'
qLearn: no visible global function definition for 'as.formula'
qLearn: no visible global function definition for 'model.frame'
qLearn: no visible global function definition for 'coef'
qLearn: no visible global function definition for 'lm'
qLearn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
Package required but not available: 'fitdistrplus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'psych', 'GPArotation', 'digest', 'knitr', 'xtable', 'shiny', 'rjson'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Formula', 'Rcpp', 'rstan', 'BH', 'RcppEigen', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'awsMethods', 'oro.nifti', 'stringr', 'aws', 'adimpro'

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 suggested but not available for checking: 'RUnit'
pcAxisCubeMake: no visible global function definition for 'aggregate'
pcAxisCubeToCSV: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Packages required but not available: 'rhli', 'lubridate', '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: 'minpack.lm', 'rgl', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'askpass', 'curl'

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', 'checkmate', 'RcppEigen'

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'calibrate'

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', 'robustbase'

Packages suggested but not available for checking:
  'shiny', 'devtools', 'shinyBS', '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', 'tidyverse', 'dplyr', '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.
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: 'shiny', 'shinythemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'leaflet', 'magrittr', 'miniUI', 'raster', 'scales',
  'shiny', 'sp'

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: 'curl', 'jsonlite', 'Rmpfr'

Package suggested but not available for checking: 'testthat'

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: 'qrcm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R.utils', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quantreg', 'SparseM', 'truncSP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'Rcpp', 'base64enc', 'png'

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', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quantreg', 'coda', 'kernlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'lqr', 'quantreg', 'psych', 'ald'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xts'

Packages suggested but not available for checking: 'knitr', 'qrmtools'

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:
  'gsl', 'mvtnorm', 'numDeriv', 'timeSeries', 'Rcpp', 'timeDate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quantmod', 'Quandl', 'zoo', 'xts', 'rugarch', 'ADGofTest'

Packages suggested but not available for checking:
  'combinat', 'copula', 'qrng', 'sfsmisc', 'RColorBrewer', 'sn',
  '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: 'randtoolbox', 'copula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'lqr', 'quantreg', 'psych', 'ald'

Package suggested but not available for checking: 'qrLMM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'cowplot', 'ggplot2', 'gridExtra', 'purrr'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'roxygen2', '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', 'RApiSerialize', 'stringfish'

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:
  'RSQLite', 'DBI', 'dplyr', 'dbplyr', 'tibble', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'glue', 'pbapply', 'processx', 'purrr', 'random', 'readr',
  'ssh', 'stringr', '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:
  'Hmisc', 'quantreg', 'BMisc', 'formula.tools', 'ggplot2', 'texreg',
  'pbapply', 'knitr', 'msm'

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', 'qtl', 'qtl2'

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: 'fst', 'qtl2'

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', 'gemma2', 'ggplot2', 'magrittr', 'Rcpp', 'rlang', 'tibble',
  'RcppEigen'

Packages suggested but not available for checking:
  'covr', 'mvtnorm', 'knitr', 'rmarkdown', 'testthat', 'broman',
  'devtools', 'qtl2', 'parallelly'

VignetteBuilder 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', 'yaml', 'jsonlite', 'data.table', 'RSQLite', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'vdiffr', 'qtl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'qtl'
Package unavailable to check Rd xrefs: 'qtl'
Running examples in 'qtlbook-Ex.R' failed
The error most likely occurred in:

> ### Name: ch3a
> ### Title: Data with a phenotype error
> ### Aliases: ch3a
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ch3a)
> 
> # phenotype problem
> pairs(ch3a$pheno)
> ch3a$pheno[ch3a$pheno[,4]==0,] # individual 159
    phe1 phe2 phe3 phe4 phe5
159   50   75   70    0   80
> 
> # individuals with similar genotypes
> library(qtl)
Error in library(qtl) : there is no package called 'qtl'
Execution halted
Packages required but not available: 'qtl', 'htmlwidgets'

Packages suggested but not available for checking:
  'htmltools', 'jsonlite', 'knitr', 'devtools', 'roxygen2',
  'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tiff', 'rgl', 'plot3D'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ci.length: no visible global function definition for 'qexp'
detectable.bc: no visible global function definition for 'uniroot'
detectable.f2: no visible global function definition for 'uniroot'
detectable.ri: no visible global function definition for 'uniroot'
nu: no visible global function definition for 'pnorm'
nullinfo: no visible global function definition for 'qnorm'
nullinfo: no visible global function definition for 'dnorm'
optselection.bc: no visible global function definition for 'optimize'
optselection.f2: no visible global function definition for 'optimize'
optspacing.bc: no visible global function definition for 'optim'
optspacing.bc: no visible global function definition for 'optimize'
optspacing.f2: no visible global function definition for 'optim'
optspacing.f2: no visible global function definition for 'optimize'
powercalc.bc: no visible global function definition for 'pchisq'
powercalc.f2: no visible global function definition for 'pchisq'
samplesize.bc: no visible global function definition for 'uniroot'
samplesize.f2: no visible global function definition for 'uniroot'
samplesize.ri: no visible global function definition for 'uniroot'
tailprob: no visible global function definition for 'pchisq'
thresh: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'qtl'
Packages required but not available:
  'shiny', 'qtl', 'Rcpp', 'openxlsx', 'stringr', 'data.table',
  'glmnet', 'doParallel', 'foreach', 'QTL.gCIMapping'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qtl', 'Rcpp', 'openxlsx', 'stringr', 'data.table', 'glmnet',
  'doParallel', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qtl', 'mnormt', 'corpcor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qtl', 'igraph', 'sem', 'graph', 'pcalg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'test_io.R'
  Comparing 'test_io.Rout' to 'test_io.Rout.save' ... OK
  Running 'test_mapqtl_io.R'
  Comparing 'test_mapqtl_io.Rout' to 'test_mapqtl_io.Rout.save' ... OK
  Running 'test_qtl.R'
  Running 'test_scanonevar.R'
  Comparing 'test_scanonevar.Rout' to 'test_scanonevar.Rout.save' ... OK
  Running 'test_tidyIO.R'
  Comparing 'test_tidyIO.Rout' to 'test_tidyIO.Rout.save' ... OK
  Running 'testaugmentation.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: 'gdata'

Package suggested but not available for checking: 'qtl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgenoud', 'quantreg', 'Rdpack', 'MatrixModels'

Packages suggested but not available for checking:
  'stringr', 'testthat', 'faraway', 'quantoptr', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmx', 'gtools', 'np', 'quantreg', 'numDeriv', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'survey', 'mice', '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: 'graph', 'RBGL', 'combinat', 'igraph'

Package suggested but not available for checking: 'Rmpfr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'matrixcalc', 'geigen'

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', 'gridBase', 'viridis', 'png', 'sp', 'geometry', 'reproj',
  'scales', 'palr'

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.
Package required but not available: 'quadprog'

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'PearsonDS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'ggplot2', 'reshape2', 'scales', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'spelling', 'lars', 'elasticnet', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'combinat'

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', 'glue', 'leaflet', 'purrr', 'rlang', 'sf'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'testthat', 'tigris', 'tidycensus', '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:
  'randtoolbox', 'assertthat', 'Rcpp', 'RcppParallel', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'maps', 'rmarkdown', 'rgl', '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:
  'httr', 'stringr', 'readr', 'jsonlite', 'assertthat', 'sjlabelled',
  'dplyr', 'tidyr', 'rlang', 'purrr', 'tibble', 'lubridate',
  'lifecycle'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'vcr', 'webmockr'

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', 'tidyr', 'ggplot2', 'GGally', 'DT'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Packages required but not available:
  'expm', 'Rfast', 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'doParallel', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'httr', 'zoo', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'timeSeries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'caret', 'dplyr', 'e1071', 'ggplot2', 'ggrepel',
  'gplots', 'readr', 'reshape2', 'rlang', 'plyr', 'pROC', 'scales',
  'stringr', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lubridate'

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: 'dr', 'MTS', 'mvtnorm', 'quantreg'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown', 'testthat', 'pracma',
  'PerformanceAnalytics', '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:
  'fastmatch', 'magrittr', 'Rcpp', 'RcppParallel', 'SnowballC',
  'stopwords', 'stringi', 'xml2', 'yaml', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat', 'formatR', 'tm', 'tokenizers',
  'knitr', 'lda', 'lsa', 'dplyr', 'purrr', 'quanteda.textmodels',
  'quanteda.textstats', 'quanteda.textplots', 'RColorBrewer', 'slam',
  'spacyr', 'stm', 'text2vec', 'topicmodels', 'jsonlite', 'quanteda',
  'tibble', 'tidytext', 'xtable', '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:
  'glmnet', 'LiblineaR', 'quanteda', 'RSpectra', 'Rcpp',
  'RcppParallel', 'SparseM', 'stringi', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ca', 'covr', 'fastNaiveBayes', 'knitr', 'lsa', 'microbenchmark',
  'naivebayes', 'quanteda.textplots', 'spelling', '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:
  'quanteda', 'extrafont', 'ggplot2', 'ggrepel', 'sna', 'igraph',
  'network', 'RColorBrewer', 'Rcpp', 'stringi'

Packages suggested but not available for checking:
  'knitr', 'quanteda.textmodels', 'quanteda.textstats', 'rmarkdown',
  'spelling', 'testthat', 'wordcloud'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quanteda', 'nsyllable', 'proxyC', 'Rcpp', 'RcppParallel', 'stringi',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'entropy', 'ExPosition', 'proxy', 'rmarkdown', 'spelling', 'svs',
  'testthat', 'knitr'

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'kableExtra', '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: 'quantreg', 'SparseM', 'np'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'units', 'errors', 'Rcpp'

Packages suggested but not available for checking:
  'pillar', 'dplyr', 'vctrs', 'tidyr', '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: 'hetGP', 'ggplot2', 'reshape2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'zoo', 'TTR', 'curl'

Packages suggested but not available for checking:
  'DBI', 'RMySQL', 'RSQLite', 'timeSeries', 'xml2', 'downloader',
  'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'GGally', 'ggplot2', 'network', 'pheatmap', 'rgl', 'sna'
Running examples in 'QuantNorm-Ex.R' failed
The error most likely occurred in:

> ### Name: QuantNorm
> ### Title: Adjust the distance matrix by quantile normalization for data
> ###   with batch effect
> ### Aliases: QuantNorm
> 
> ### ** Examples
> 
> 
> library(pheatmap) #drawing heatmap
Error in library(pheatmap) : there is no package called 'pheatmap'
Execution halted
Packages required but not available:
  'stringr', 'rgenoud', 'quantreg', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randomForest', 'RColorBrewer'

Packages suggested but not available for checking:
  'gss', '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:
  'quantreg', 'mnormt', 'fda', 'Rearrangement'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ranger'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SparseM', 'MatrixModels', 'conquer'

Packages suggested but not available for checking:
  'tripack', 'akima', 'rgl', 'logspline', 'nor1mix', 'Formula', 'zoo',
  '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:
  'quantreg', 'abind', 'zoo', 'snowfall', '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:
  'data.table', 'fasttime', 'RCurl', 'readxl', 'Rcpp', 'R6'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'doParallel', 'gridExtra', 'ggplot2', 'NbClust',
  'DEoptim', 'optimx', 'fpc'

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: 'neuralnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'Rdpack', 'Ternary', 'TreeTools', 'viridisLite', 'Rcpp'

Packages suggested but not available for checking:
  'bookdown', 'knitr', 'phangorn', 'Rcpp', 'rmarkdown', 'testthat',
  'usethis', '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: 'rmarkdown', '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: 'edgeR', 'pracma'

Packages suggested but not available for checking: 'BB', 'nleqslv'

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:
  'shiny', 'miniUI', 'rstudioapi', 'highr', 'styler', 'classInt',
  'htmltools', 'labelled'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'dplyr', 'ggplot2', 'tidyr', 'janitor',
  'forcats', 'knitr', 'rmarkdown', 'survey', 'Hmisc'

VignetteBuilder 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', 'tidyr', 'dplyr', 'RcppArmadillo'

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: 'numbers'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'distances', 'scclust'

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', 'readr', 'curl', 'tibble'

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', 'sp', 'rgeos', 'rgdal', 'httr', 'sf'

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: 'distances', 'sandwich', 'scclust'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'data.table', 'fpCompare', 'ggplot2', 'gridBase',
  'igraph', 'raster', 'RColorBrewer', 'rgdal', 'rgeos', 'sp'

Packages suggested but not available for checking:
  'covr', 'fastshp', 'hunspell', 'knitr', '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: 'DEoptim', 'dplyr', 'ggplot2', 'MPDiR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rlang', 'psych', 'nortest', 'dplyr'

Packages suggested but not available for checking:
  'ggthemes', '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: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ape'

Packages suggested but not available for checking: 'spider', 'adegenet'

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: 'partykit', '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.
Packages required but not available:
  'quantreg', 'purrr', 'magrittr', 'ALDqr', 'bayesQR', 'MCMCpack',
  'ggplot2', 'knitr', 'gridExtra', 'GIGrvg', 'dplyr', 'tidyr',
  'robustbase', 'ald'

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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dplyr', 'testthat'
Note: found 12928 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: 'glmnet', 'lars', 'flare'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'relimp'

Package which this enhances but not available for checking: 'psychotools'
Package unavailable to check Rd xrefs: 'psychotools'
Packages required but not available:
  'dplyr', 'ggplot2', 'knitr', 'Rcpp', 'rlang', 'xfun', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rbenchmark', '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: 'fda'
Running examples in 'QZ-Ex.R' failed
The error most likely occurred in:

> ### Name: fda.geigen
> ### Title: Generalized Eigen Analysis as in fda Package
> ### Aliases: fda.geigen
> ### Keywords: programming
> 
> ### ** Examples
> 
> library(QZ, quiet = TRUE)
> 
> A <- matrix(as.double(1:6), 2)
> B <- matrix(as.double(c(2, 1, 1, 2)), 2)
> C <- diag(as.double(1:3))
> 
> ret.qz <- fda.geigen(A, B, C)
> 
> ### Verify
> library(fda, quiet = TRUE)
Error in library(fda, quiet = TRUE) : there is no package called 'fda'
Execution halted
mutualCoherence : .setOneMutualP: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available:
  'jsonlite', 'ggplot2', 'dplyr', 'pinyin', 'maps'

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:
  'ahaz', 'pracma', 'zoo', 'caTools', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coda'

Packages suggested but not available for checking:
  'bbmle', 'lme4', 'ggplot2', 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/R2admb.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BayesXsrc', 'colorspace'

Packages suggested but not available for checking:
  'akima', 'coda', 'maps', 'maptools', 'MBA', 'shapefiles', 'sp',
  'spdep', 'rgdal', 'spData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'sampling', 'devtools'

Package suggested but not available for checking: 'ReGenesees'

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.
Packages required but not available:
  'htmlwidgets', 'htmltools', 'jsonlite', 'rstudioapi'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R6', 'shiny', 'shinytest', 'testthat',
  'webshot'

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: 'stringr', 'rstudioapi'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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:
  'dplyr', 'glue', 'magrittr', 'r2dii.data', 'rlang', 'tidyr',
  'tidyselect', 'zoo'

Packages suggested but not available for checking:
  'covr', 'r2dii.match', 'rmarkdown', 'roxygen2', 'spelling',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'rlang', 'rmarkdown', 'testthat'
Note: found 34 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:
  'data.table', 'dplyr', 'glue', 'magrittr', 'purrr', 'r2dii.data',
  'rlang', 'stringdist', 'stringi', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgdal', 'sp', 'matrixStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'plyr', 'devFunc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lmerTest', 'pbkrtest', 'ggplot2', 'afex', 'gridExtra', 'data.table',
  'dplyr'

Packages suggested but not available for checking: 'lme4', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rjags', 'abind', 'coda', 'R2WinBUGS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'broomExtra', 'dplyr', 'magrittr', 'rlang', 'stringr',
  'tidyselect'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R2WinBUGS', 'digest', 'texreg', 'foreach', 'doParallel', 'coda',
  'memisc', 'broom', 'tibble'

Packages suggested but not available for checking:
  'doBy', 'car', 'lmtest', 'mitools', 'reshape'

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 suggested but not available for checking:
  'caret', 'e1071', 'earth', 'evtree', 'glmnet', 'mlbench', 'mlr',
  'partykit', 'randomForest', 'ranger', 'xgboost'
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'stringi', 'knitr', 'rmarkdown', 'testthat', 'emmeans', 'dplyr',
  'tidyr', 'devtools', 'covr', 'ggplot2', 'haven'
Running examples in 'r2rtf-Ex.R' failed
The error most likely occurred in:

> ### Name: rtf_body
> ### Title: Add Table Body Attributes to the Table
> ### Aliases: rtf_body
> 
> ### ** Examples
> 
> library(dplyr) # required to run examples
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
Packages required but not available: 'stringr', 'magrittr'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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: 'rmumps', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'RcppXPtrUtils', 'slam', 'RUnit', 'deSolve', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sysfonts'

Packages suggested but not available for checking: 'XML', 'Cairo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'qpdf'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'RMark'

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: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: 'coda'

Package suggested but not available for checking: 'BRugs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 's20x', 'leaps', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'magrittr', 'bio3d'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shiny', 'colourpicker', '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
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp', 'testthat', 'roxygen2',
  'BayesianTools', 'sensitivity', 'dplyr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'R.rsp'
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', 'reshape2', 'whisker', 'tinytex'

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.
Packages required but not available: 'bitops', 'RCurl', 'RJSONIO'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'here', 'magick', 'magrittr', 'pROC',
  'psych', 'purrr'

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:
  'coda', 'corpcor', 'gdata', 'gplots', 'gtools', 'pso', 'truncnorm',
  'kableExtra'

Packages suggested but not available for checking:
  'maps', 'testthat', '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:
  'dplyr', 'tibble', 'httr', 'xml2', 'assertthat'

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:
  'checkmate', 'curl', 'data.table', 'httr', 'jdx', 'rJava', 'sf',
  'sfheaders'

Packages suggested but not available for checking:
  'akima', 'covr', 'dplyr', 'ggplot2', 'knitr', 'mapview', '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: 'data.table'

Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'R6'

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', '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: 'R6', 'magrittr', 'digest', 'hellno'

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:
  'glue', 'rstudioapi', 'miniUI', 'shiny', 'dplyr', 'magrittr',
  'stringr', 'purrr'

Packages suggested but not available for checking: 'R6', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'purrr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'collections', 'dplyr', 'DBI', 'RSQLite', 'ggplot2',
  'tibble', 'tidyr', 'pryr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'knitr', 'microbenchmark', 'pryr', 'testthat', 'ggplot2', 'scales'
'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: 'bayesmeta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'reshape2', 'plotly', 'gtools', 'cowplot',
  'dendextend', 'data.table', 'plyr', 'ggdendro', 'gridExtra',
  'alakazam', 'tigger', 'htmlwidgets', 'gtable', 'rlang',
  'RColorBrewer', 'tidyr', 'stringi', 'splitstackshape', 'fastmatch'

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:
  'numbers', 'polynom', 'shiny', 'stringdist'

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:
  'coop', 'FateID', 'FNN', 'fpc', 'ggplot2', 'ica', 'igraph', 'irlba',
  'locfit', 'matrixStats', 'pheatmap', 'propr', 'quadprog',
  'randomForest', 'Rcpp', 'RColorBrewer', 'Rtsne', 'umap', 'vegan'

Packages suggested but not available for checking:
  'batchelor', 'DESeq2', 'knitr', 'rmarkdown', 'SummarizedExperiment'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fasterize', 'plotwidgets', 'raster', 'rgdal', 'sf', 'Rcpp', 'comat',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'dplyr', 'pbapply', 'testthat', 'knitr', 'rmarkdown', 'RColorBrewer',
  '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:
  'matrixStats', 'rstudioapi', 'plotrix', 'maps', 'maptools', 'ncdf4',
  'rgdal', 'rgeos', 'sp', 'raster'

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: 'sfsmisc', '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 suggested but not available for checking: 'ggplot2'
Packages required but not available: 'htmlwidgets', 'htmltools'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyr', '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:
  'lme4', 'ggplot2', 'matrixStats', 'reshape2', 'lmerTest', 'e1071',
  'tidyr', 'stringr', 'dplyr', 'Hmisc', 'gridExtra', 'forestplot',
  'knitr', 'openxlsx', 'car'

Package suggested but not available for checking: 'markdown'

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.
Note: found 4 marked UTF-8 strings
Package suggested but not available for checking: 'radsafer'
Packages required but not available:
  'import', 'ggplot2', 'tidyr', 'dplyr', 'miniUI', 'shiny', 'shinyjs',
  'caret', 'rlang', 'shinyscreenshot'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'clValid'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'radiant.data', 'ggplot2', 'scales', 'dplyr', 'tidyr', 'magrittr',
  'shiny', 'psych', 'import', 'lubridate', 'polycor', 'patchwork'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'ggplot2', 'lubridate', 'tidyr', 'dplyr', 'tibble',
  'rlang', 'broom', 'car', 'knitr', 'markdown', 'rmarkdown', 'shiny',
  'jsonlite', 'shinyAce', 'psych', 'DT', 'readr', 'readxl', 'writexl',
  'scales', 'curl', 'rstudioapi', 'import', 'plotly', 'glue',
  'shinyFiles', 'stringi', 'randomizr', 'patchwork', 'base64enc'

Packages suggested but not available for checking:
  'svglite', 'DBI', 'RSQLite', 'RPostgreSQL', 'odbc', 'webshot',
  'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'radiant.data', 'mvtnorm', 'dplyr', 'magrittr', 'shiny', 'AlgDesign',
  'import', 'pwr', 'randomizr', 'polycor'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'radiant.data', 'radiant.basics', 'shiny', 'NeuralNetTools',
  'sandwich', 'car', 'ggplot2', 'data.tree', 'stringr', 'lubridate',
  'tidyr', 'dplyr', 'rlang', 'magrittr', 'DiagrammeR', 'import',
  'psych', 'e1071', 'ggrepel', 'broom', 'patchwork', 'ranger',
  'xgboost', 'pdp', 'yaml'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'radiant.data', 'radiant.model', 'shiny', 'dplyr', 'rlang',
  'ggplot2', 'scales', 'magrittr', 'psych', 'GPArotation', 'car',
  'import', 'ggrepel', 'lubridate', 'polycor', 'gower', 'clustMixType',
  'patchwork'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model',
  'radiant.multivariate', 'shiny', 'import'

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.
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par points polygon read.table sd segments
  text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package required but not available: 'hermite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rmarkdown', 'bookdown', 'xfun', 'htmltools', 'jsonlite',
  'lubridate', 'png', 'mime', 'rstudioapi', 'rprojroot', 'xml2',
  'base64enc', 'whisker', 'downloader', 'progress', 'stringr', 'knitr',
  'digest', 'yaml'

Packages suggested but not available for checking:
  'htmlwidgets', 'r2d3', 'DiagrammeR', 'shiny', 'rsconnect', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'lexicon', '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:
  'quadprog', 'plyr', 'magrittr', 'MCMCpack'

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.
Packages required but not available:
  'rgl', 'geometry', 'oro.dicom', 'ptinpoly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glue', 'httr', 'readr', 'checkmate', 'curl'

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: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'readr', 'RadData', 'stringr', 'magrittr', 'dplyr',
  'rlang', 'scatterplot3d', 'ggthemes', 'qpdf', 'utf8'

Packages suggested but not available for checking:
  'testthat', 'beepr', '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: 'ReacTran', 'rootSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'rlang', 'igraph', 'pracma', 'hexbin', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bodenmiller', 'tidyr', 'RColorBrewer',
  'cytofan', '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: 'RCurl', '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:
  'lars', 'foreach', 'doParallel', 'glmnet', 'fastcmprsk'

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: 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'systemfonts', 'textshaping'

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:
  'htmltools', 'htmlwidgets', 'crosstalk', 'knitr'

Packages suggested but not available for checking:
  'jsonlite', 'rmarkdown', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'expm', 'reshape', 'ggplot2', 'Hmisc', 'fdrtool',
  'snowfall', 'sfsmisc', 'gRbase', 'RBGL', 'graph', 'Rcpp', 'RSpectra',
  'RcppArmadillo'

Packages suggested but not available for checking: 'KEGGgraph', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'rags2ridges', 'abind', 'expm', 'fdrtool', 'mvtnorm',
  'Biobase', 'CGHbase', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'limSolve', 'futile.logger'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown', 'reshape2', 'stringr',
  'ggplot2', 'RColorBrewer', 'BondValuation', 'R.cache', 'Quandl'

VignetteBuilder 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', 'httr', 'jsonlite', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pcaPP', 'hdrcde', 'colorspace', 'ks'

Package suggested but not available for checking: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'pbmcapply', 'optimx', 'ape', 'stringr', 'pegas', 'ggplot2',
  'ggtree', 'scatterpie', 'phylobase', 'haplotypes', 'rrBLUP', 'expm',
  'here', 'htmlwidgets', 'Rfast', 'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plotly'

VignetteBuilder 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', 'popdemo'

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', 'readr', '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: 'ggplot2', 'doParallel', 'foreach'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'cowplot', 'reshape2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ipfp', 'wrswoR'

Packages suggested but not available for checking: 'testthat', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'xml2', 'tidyr', 'dplyr', 'stringr', 'robotstxt', 'crayon',
  'curl', 'stringi'

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:
  'data.table', 'openxlsx', 'Hmisc', 'stringr', 'gdata', 'readr',
  'stringi', 'shiny', 'shinydashboard', 'DT', 'shinyjs', 'shinyFiles'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'rlist'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'covr', 'knitr', 'magrittr', 'purrr',
  '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'

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: 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'htmlwidgets', 'reactR', 'shiny', 'jsonlite',
  'lubridate', 'minpack.lm', 'base64enc', 'xml2', 'stringr'

Package suggested but not available for checking: 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'htmltools', 'data.table', 'pipeR', 'knitr', 'yaml',
  'zoo'

Packages suggested but not available for checking:
  'magrittr', 'shiny', 'testthat', 'shinydashboard', 'base64enc',
  'lubridate', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dynamicTreeCut', 'fastcluster', 'ff', 'InterpretMSSpectrum',
  'BiocManager', 'httr', 'jsonlite', 'preprocessCore', 'e1071',
  'gplots', 'pcaMethods', 'stringr', 'xml2', 'webchem', 'stringi',
  'RCurl', 'MSnbase', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xcms'

VignetteBuilder 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:
  '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:
  'httr', 'urltools', 'lubridate', 'dplyr', 'jsonlite', 'magrittr'

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'

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:
  'cli', 'crayon', 'httr', 'rappdirs', 'readxl'

Packages suggested but not available for checking:
  'covr', 'testthat', 'httptest', '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: 'lavaan', 'ellipse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'maps', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vegan', 'ggplot2', 'RColorBrewer', 'gplots', 'plyr', 'reshape2',
  'scales', 'labdsv', 'gridExtra', 'ggmap', 'permute', 'VennDiagram',
  'data.table', 'FD', 'RgoogleMaps', 'reshape', 'ade4', 'phangorn',
  'phytools', 'ape'

Packages suggested but not available for checking:
  'testthat', 'mapproj', 'gtable', 'indicspecies', 'Heatplus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xml2', 'base64enc', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyverse', 'plotly', 'openxlsx',
  'DBI', 'RSQLite', '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: 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tibble', '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:
  'entropy', 'AUC', 'poweRlaw', 'RSpectra', 'irlba'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'snowfall', 'orthopolynom', 'polynom', 'fourierin', 'sfsmisc',
  'tmvtnorm', 'rdetools', 'ks', 'statmod', 'RCEIM', 'robustbase',
  'VGAM'

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/RandomCoefficients.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colorspace', 'stringr', 'V8', 'scales', 'Rtsne'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sp', 'RandomFieldsUtils'

Packages suggested but not available for checking:
  'colorspace', 'RColorBrewer', 'mvtnorm', 'raster', 'tcltk2',
  'tkrplot', 'spam', 'minqa', 'soma', 'optimx', 'nloptr', 'pso',
  'GenSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'spam', 'RandomFields'
Packages required but not available:
  'data.table', 'dplyr', 'DT', 'GGally', 'ggplot2', 'ggrepel',
  'randomForest', 'ranger', 'reshape2', 'rmarkdown'

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: 'RColorBrewer'
Packages required but not available:
  'BRISC', 'matrixStats', 'randomForest', 'pbapply'

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: 'data.tree', 'DiagrammeR'

Packages suggested but not available for checking:
  'pec', 'prodlim', 'mlbench', 'akima', 'caret', 'imbalance'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'permute', 'matrixStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotrix'

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/article.Rnw'
   'inst/doc/comparison-example.Rnw'
   'inst/doc/desirability-example.Rnw'
   'inst/doc/randomizeR-refCard.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'dplyr', 'blockTools', 'testthat', 'rmarkdown', 'ri'

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:
  'fastGHQuad', 'Rfast', 'doParallel', 'doRNG', 'foreach'

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: 'crayon', 'data.table', 'toOrdinal'

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:
  'psych', 'nFactors', 'mvtnorm', 'sfsmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ParamHelpers', 'smoof', 'checkmate', 'parallelMap', 'fs'

Packages suggested but not available for checking:
  'emoa', 'rmarkdown', 'testthat', 'knitr', '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', 'doParallel', 'iterators', 'foreach', 'ggplot2', 'pROC',
  'gtools'

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', 'glue', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'spelling', 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jsonlite', 'xml2', 'curl', 'httr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
bartels.rank.test: no visible global function definition for 'na.omit'
bartels.rank.test: no visible global function definition for 'pbeta'
bartels.rank.test: no visible global function definition for 'pnorm'
cox.stuart.test: no visible global function definition for 'pbinom'
difference.sign.test: no visible global function definition for
  'na.omit'
difference.sign.test: no visible global function definition for 'pnorm'
rank.test: no visible global function definition for 'na.omit'
rank.test: no visible global function definition for 'pnorm'
rruns: no visible global function definition for 'runif'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'na.omit'
runs.test: no visible global function definition for 'points'
runs.test: no visible global function definition for 'abline'
runs.test: no visible global function definition for 'gray'
runs.test: no visible global function definition for 'pnorm'
turning.point.test: no visible global function definition for 'embed'
turning.point.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Package required but not available: 'rngWELL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'distr', 'distrEx', 'startupmsg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'raster', 'rgdal', 'alphahull', 'stringi', 'rgeos', 'pbapply',
  'cleangeo', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glue', 'future', 'future.apply', 'progressr', 'sf', 'RSQLite',
  'DBI', 'magrittr', 'data.table', 'raster', 'exactextractr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'viridis', 'rmarkdown', 'pkgdown',
  'igraph', 'spdep'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'concaveman', 'dplyr', 'maps', 'maptools', 'rnaturalearthdata',
  'raster', 'rgdal', 'rgeos', 'rgl', 'scales', 'sf', '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.
Packages required but not available:
  'dplyr', 'jsonlite', 'raster', 'rgbif', 'rgdal', 'rgeos', 'shiny',
  'sp', 'spatstat', 'spocc', 'spThin'

Packages suggested but not available for checking:
  'BIEN', 'biomod2', 'dismo', 'ecospat', 'ENMeval', 'googlesheets',
  '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: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jpeg', 'shiny', 'tidyverse'

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: 'knitr'
Package required but not available: 'gtools'

Packages suggested but not available for checking:
  'xtable', 'kohonen', 'mclust', 'clValid'

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: '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', 'hash', 'optimx', 'permute'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coin'

Package suggested but not available for checking: 'RGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rms'
Running examples in 'rankhazard-Ex.R' failed
The error most likely occurred in:

> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called 'rms'
Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tikzDevice', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'
Malformed Description field: should contain one or more complete sentences.
rank.L2R: no visible global function definition for 'kmeans'
rank.L2R: no visible global function definition for 'pnorm'
rank.LN: no visible global function definition for 'kmeans'
rank.LN: no visible global function definition for 'pnorm'
rank.gs: no visible global function definition for 'qnorm'
rank.wald: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
Packages required but not available:
  'graph', 'RBGL', 'limma', 'NetPreProc', 'PerfMeas'

Package suggested but not available for checking: 'bionetdata'

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:
  'DBI', 'devtools', 'digest', 'gistr', 'httr', 'knitr', 'magrittr',
  'readr', 'RJDBC', 'RMariaDB', 'sendmailR', 'shiny', '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: 'jsonlite', 'httr', 'yaml'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  datetime.c:724:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:725:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:763:3: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:971:6: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1115:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1116:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1199:7: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RApiDatetime/RApiDatetime.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package required but not available: 'jsonlite'

Package suggested but not available for checking: 'plumber'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'RCurl', 'curl', 'GenomicRanges', 'IRanges', 'bigsnpr'

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', 'RANN', 'PBSmapping', 'RgoogleMaps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'Biostrings', 'Rsamtools', 'GenomicRanges',
  'GenomicAlignments', 'PropCIs'

Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg19'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: 'unix'
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'covr', 'withr'
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: 'reshape', 'plyr', 'pander'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'yaml', 'stringr', 'rapportools', 'pander'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'stringr', 'retry', 'dplyr', 'tidyr', 'lgr'

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.
fnRAP: no visible global function definition for 'chisq.test'
fnRAP: no visible global function definition for 'combn'
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available:
  'jsonlite', 'tibble', 'magrittr', 'tidyr', 'dplyr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyverse'

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 required but not available:
  'sp', 'raster', 'assertthat', 'PBSmapping', 'scales', 'shape',
  'adehabitatHR', 'RgoogleMaps', 'RandomFields', 'RColorBrewer',
  'plyr', 'doParallel', 'rgeos', 'rgdal', 'hypervolume', 'ks',
  'mvtnorm', 'ggplot2', 'Rcpp', 'RcppEigen', 'BH'

Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'rmarkdown', 'dplyr', 'vegan', 'gurobi',
  'gridExtra', 'rgl', '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', 'glue', 'gtools', 'httr', 'jsonlite', 'lubridate',
  'magrittr', 'purrr', 'stringr', 'tibble', 'rlang', 'lifecycle'

Packages suggested but not available for checking:
  'desc', 'devtools', 'goodpractice', 'knitr', 'lintr', 'roxygen2',
  'rmarkdown', 'testthat', 'usethis', '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:
  'Rdpack', 'magrittr', 'dplyr', 'pracma', 'gsl'

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.
Packages required but not available:
  'ade4', 'adiv', 'ape', 'dplyr', 'geiger', 'vegan'

Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'phyloregion', 'picante', 'phytools',
  'raster', '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: 'survey'

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: 'glmnet', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'dendextend', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'arm'
Package required but not available: 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RSpectra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'document', 'fritools', 'gert', 'highr', 'knitr',
  'reticulate'

Packages suggested but not available for checking:
  'devtools', 'pkgload', 'rasciidoc', 'rmarkdown', 'rprojroot',
  'RUnit', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'RSNNS', 'e1071', 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'doParallel', 'e1071', 'foreach', 'randomForest', 'ggplot2',
  'gridExtra', 'formatR', 'FNN', 'ranger', 'KernelKnn'

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:
  'raster', 'proxy', 'foreach', 'progress', 'svMisc'

Packages suggested but not available for checking:
  'doParallel', 'knitr', 'rmarkdown', 'rasterVis', 'RColorBrewer',
  'gridExtra', 'gstat'

VignetteBuilder 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', 'data.table', 'fasterize', 'sf'

Packages suggested but not available for checking: 'rasterVis', 'rgdal'

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.
Package required but not available: 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'raster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'raster'

Packages suggested but not available for checking:
  'lmom', 'testthat', 'sp', 'soilwater'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'data.table', 'rlang', 'plotly', 'ggplot2', 'magrittr'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'lubridate'

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: 'png'

Packages suggested but not available for checking:
  'covr', 'lintr', 'pkgdown', 'ragg', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sp', 'Rcpp'

Packages suggested but not available for checking:
  'rgdal', 'rgeos', 'ncdf4', 'igraph', 'rasterVis', 'sf', 'tinytest',
  'gstat', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'terra', 'latticeExtra', 'RColorBrewer', 'hexbin', 'sp',
  'zoo', 'viridisLite'

Packages suggested but not available for checking:
  'rgl', 'ggplot2', 'colorspace', 'dichromat', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'glpkAPI', 'lpSolveAPI', 'Rirt', 'reshape2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'assertthat'

Packages suggested but not available for checking:
  'testthat', 'microbenchmark', '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:
  'ape', 'geiger', 'coda', 'corpcor', 'phylolm', 'readr', 'mvMORPH',
  'Rcpp', 'ellipse', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'phytools', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
rateratio.test: no visible global function definition for
  'complete.cases'
rateratio.test: no visible global function definition for 'pbinom'
rateratio.test : p.L: no visible global function definition for 'qbeta'
rateratio.test : p.U: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppParallel', 'ggplot2', 'rlang',
  'loo', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'coda', 'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
concordance: no visible global function definition for 'quantile'
concordance : Normal: no visible global function definition for 'qnorm'
concordance : Normal: no visible global function definition for 'pnorm'
concordance : MC: no visible global function definition for 'rmultinom'
concordance : MC: no visible global function definition for 'quantile'
concordance: no visible global function definition for 'qnorm'
concordance: no visible global function definition for 'pnorm'
concordance : Chisq: no visible global function definition for 'qchisq'
concordance : Chisq: no visible global function definition for 'pchisq'
concordance : Normal2: no visible global function definition for
  'qnorm'
concordance : Normal2: no visible global function definition for
  'pnorm'
concordance : MC2: no visible global function definition for
  'rmultinom'
concordance : MC2: no visible global function definition for 'quantile'
wlin.conc: no visible global function definition for 'quantile'
wlin.conc : MC: no visible global function definition for 'rmultinom'
wlin.conc : MC: no visible global function definition for 'quantile'
wquad.conc: no visible global function definition for 'quantile'
wquad.conc : MC: no visible global function definition for 'rmultinom'
wquad.conc : MC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
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: 'ggplot2', 'gridExtra', 'quantreg'

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/RDperm.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'DBI', 'reticulate', 'uuid'

Packages suggested but not available for checking:
  'arrow', 'bit64', 'dplyr', 'dbplyr', 'testthat', 'tibble', 'vroom',
  'covr', 'knitr', 'rmarkdown', '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: 'pROC', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'snowfall'

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/RationalExp.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'polynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'ggsci', 'hms', 'lubridate',
  'magrittr', 'plyr', 'rjson', 'stringr', 'tidyr'

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.
Package suggested but not available for checking: 'rattle'
Packages required but not available:
  'tibble', 'bitops', 'ggplot2', 'magrittr', 'stringi', 'stringr',
  'tidyr', 'dplyr', 'XML', 'rpart.plot'

Packages suggested but not available for checking:
  'pmml', 'colorspace', 'ada', 'amap', 'arules', 'arulesViz',
  'biclust', 'cairoDevice', 'cba', 'corrplot', 'descr', 'doBy',
  'e1071', 'ellipse', 'fBasics', 'fpc', 'gdata', 'ggdendro', 'ggraptR',
  'gplots', 'gridExtra', 'gtools', 'hmeasure', 'Hmisc', 'kernlab',
  'mice', 'party', 'plyr', 'psych', 'randomForest', 'RColorBrewer',
  'readxl', 'reshape', 'rggobi', 'RGtk2', 'ROCR', 'RODBC', 'scales',
  'SnowballC', 'timeDate', 'tm', 'verification', 'wskm', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'gaston', 'mlogit', 'Formula', 'dfidx',
  'RcppEigen', '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:
  'data.table', 'yaml', 'hdf5r', 'fst', 'dipsaus', 'R.matlab', 'glue',
  'later', 'stringr', 'rlang', 'edfReader', 'lazyarray', 'ini',
  'jsonlite', 'R6'

Packages suggested but not available for checking:
  'pryr', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'dplyr', 'tibble', 'purrr', 'tidyr'

Packages suggested but not available for checking: 'spelling', '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:
  'colorspace', 'cowplot', 'deldir', 'dplyr', 'dygraphs', 'gdata',
  'ggplot2', 'igraph', 'lubridate', 'magrittr', 'ncdf4', 'purrr',
  'reshape2', 'rgdal', 'rgeos', 'scales', 'sf', 'sp', 'xts', 'zoo'

Packages suggested but not available for checking:
  'devtools', 'magick', 'knitr', 'weathercan', 'tidyhydat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'XML', 'RCurl', 'scrapeR', 'gdata', 'scales', 'rgdal',
  'maptools', 'raster', 'sp'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'ROCR', 'ggplot2', 'tidyr'

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:
  'actuar', 'ChainLadder', 'dplyr', 'devtools', 'FinCal',
  'fitdistrplus', 'forcats', 'ggplot2', 'insuranceData', 'knitr',
  'Lahman', 'lubridate', 'maps', 'mondate', 'nycflights13', 'purrr',
  'randomForest', 'randomNames', 'readr', 'readxl', 'RColorBrewer',
  'rmarkdown', 'scales', 'stringr', 'tibble', 'tidyr', 'tweedie', 'XML'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'rvest', 'dplyr', 'jsonlite', 'xml2', 'stringr', 'clipr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', 'tibble', '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:
  'Rcpp', 'png', 'magrittr', 'jpeg', 'RcppArmadillo', 'progress'

Packages suggested but not available for checking: 'magick', 'raster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'assertthat', 'tibble', 'magrittr', 'purrr', 'png', 'raster',
  'decido', 'rayimage', 'progress', 'RcppThread', 'spacefillr'

Packages suggested but not available for checking:
  'sf', 'spData', 'dplyr', 'Rvcg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'Rcpp', 'progress', 'raster', 'scales',
  'png', 'magrittr', 'rgl', 'terrainmeshr', 'rayimage', 'RcppArmadillo'

Packages suggested but not available for checking:
  'reshape2', 'viridis', 'av', 'magick', 'ggplot2', 'sf', 'rayrender',
  'isoband', 'maptools', 'geosphere'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ncdf4', 'sf', 'units'

Packages suggested but not available for checking:
  'testthat', 'covr', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crul', 'xml2', 'data.table', 'tibble'

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: 'IntCal', 'coda', 'Rcpp'

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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'RCurl', 'dplyr', 'openssl', 'stringr', 'magrittr', 'tibble',
  '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:
  'data.table', 'magrittr', 'foreach', 'GPfit'

Package suggested but not available for checking: 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'pkgload', 'rmarkdown', 'RUnit', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'runit.R'
Running the tests in 'tests/runit.R' failed.
Last 13 lines of output:
  +   stop(
  +     "Can not find RUnit test directory ", unit_dir,
  +     ". Try to (re)install the package first."
  +   )
  + }
  > setup_file <- file.path(unit_dir, "setup.R")
  > if (file.exists(setup_file)) source(setup_file)
  > package_suite <- RUnit::defineTestSuite("rBDAT_unit_test",
  +   dirs = unit_dir,
  +   testFileRegexp = "^runit.*\\.[rR]",
  +   testFuncRegexp = "^test_+"
  + )
  Error in loadNamespace(x) : there is no package called 'RUnit'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'XML', 'RCurl', 'rjson', 'wordcloud', 'rtematres', 'RColorBrewer'

Packages suggested but not available for checking: 'ggplot2', 'plyr'

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:
  'ggplot2', 'dplyr', 'magrittr', 'tidyr', 'purrr', 'lme4', 'forcats',
  'sf', 'lubridate', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'ggmap', 'knitr', 'glue', 'rmarkdown', 'testthat', 'tidygraph',
  '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:
  'Rcpp', 'assertthat', 'mvtnorm', 'Formula', 'checkmate', 'rstan',
  'bayesplot', 'ggplot2', 'dplyr', 'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', 'foreach', 'purrr', 'rstanarm',
  'scales', 'broom', 'tidyr', 'rstantools'

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: 'MCMCpack', 'gtools'
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gam', 'RobStatTM'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'raster', 'sp', 'dplyr', 'geosphere', 'rlang', 'reproj', 'sfheaders'

Packages suggested but not available for checking:
  'bgmfiles', 'covr', '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: 'rJava', 'imager', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'xml2', 'jsonlite', 'plyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'vcr'

VignetteBuilder 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', 'future', 'future.apply', 'ggplot2', 'magrittr',
  'nls2', 'polynom'

Packages suggested but not available for checking:
  'ggpubr', 'knitr', 'lintr', 'microbenchmark', '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'
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:
  'rbi', 'data.table', 'lubridate', 'reshape2'

Packages suggested but not available for checking:
  'R.rsp', 'testthat', 'covr', 'stringi'

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', 'ggplot2'

Packages suggested but not available for checking:
  'covr', 'knitr', 'miniUI', 'rmarkdown', 'rstudioapi', 'shiny',
  '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:
  'magrittr', 'plyr', 'Rcpp', 'RcppParallel', 'R.utils', 'rjson',
  'slam', 'openxlsx'

Packages suggested but not available for checking:
  'ape', 'reshape2', 'rhdf5', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'curl'

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: 'RCurl', 'RJSONIO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'ncdf4', 'processx', 'reshape2'

Packages suggested but not available for checking:
  'coda', 'covr', 'R.rsp', 'stringi', 'testthat', 'ggplot2'

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:
  'plyr', 'crul', 'ggplot2', 'mapproj', 'sp', 'dplyr', 'jsonlite',
  'data.table', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'taxize', 'vcr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RJSONIO', 'RCurl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'RCurl', 'digest', 'RJSONIO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'getPass', 'httr', 'jsonlite', 'png', '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.
Package required but not available: 'R6'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', '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.
Package required but not available: 'bnlearn'

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:
  'fts', 'xts', 'zoo', 'data.table', 'knitr', 'rmarkdown', 'minidown',
  '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:
  'hdf5r', 'data.table', 'xts', 'dygraphs', '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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'bnlearn', 'igraph'
Packages required but not available:
  'data.table', 'httr', 'rjson', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'lubridate', 'readxl', '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:
  'htmlwidgets', 'maps', 'jsonlite', 'digest', 'hexbin', 'lazyeval',
  'pryr', 'magrittr', 'ggplot2', 'scales', 'gistr'

Packages suggested but not available for checking:
  'testthat', 'data.table', 'lintr', 'roxygen2', 'latticeExtra',
  'knitr', 'rmarkdown'

Package which this enhances but not available for checking: '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: 'Rcpp', 'data.table', 'digest'

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: 'Matching'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'BBmisc', 'checkmate', 'shape', 'TeachingDemos'

Packages suggested but not available for checking: 'testthat', 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', '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: '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: 'rjson', 'httr', 'openssl', 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mice', 'psych'

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.
Package required but not available: 'devtools'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rlang'

Packages suggested but not available for checking: 'ebal', 'survey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.methodsS3', 'R.oo', 'R.utils', 'digest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'splancs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'trust'

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 required but not available: 'data.table', 'ggplot2', 'scales'

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', 'rgdal'

Packages suggested but not available for checking: 'prettymapr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'spatstat.geom', 'spatstat.core', 'spatstat.linnet',
  'spatstat', 'snow', 'doSNOW', 'foreach', 'iterators', 'knitr'

Packages suggested but not available for checking:
  'spelling', '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: 'interp', 'matrixStats'

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', 'gplots'

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:
  'covr', 'testthat', 'vdiffr', 'sf', 'spData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
RC.read.table: no visible global function definition for 'type.convert'
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
Packages required but not available: 'pracma', 'rgdal', 'sp'

Packages suggested but not available for checking:
  'rgeos', 'rgbif', 'knitr', 'rmarkdown', 'R.rsp', 'testthat',
  '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: 'plyr'

Packages suggested but not available for checking: 'optmatch', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rJava', 'arules', 'R.utils', 'TunePareto'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rmosek', 'REBayes', 'orthopolynom', 'Formula', 'mvtnorm'

Packages suggested but not available for checking: 'knitr', 'digest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

Packages suggested but not available for checking:
  'rcbalance', 'optmatch', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rccmisc'

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: 'dplyr'

Packages suggested but not available for checking:
  'checkpoint', 'testthat', 'R.rsp', 'rvest', 'xml2'

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: 'rJava'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rcdklibs', 'fingerprint', 'rJava', 'png', 'iterators', 'itertools'

Packages suggested but not available for checking:
  'xtable', 'RUnit', '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:
  'Rcpp', 'git2r', 'httr', 'testthat', 'devtools', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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:
  'data.table', 'igraph', 'sqldf', 'visNetwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', 'ncdf4', 'raster', 'sp'

Package suggested but not available for checking: 'testthat'

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: 'rmarkdown', 'knitr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'V8', 'R6', 'ggplot2', 'plyr', 'dplyr', 'assertthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rdpack', 'reticulate'

Package suggested but not available for checking: 'testthat'

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:
  'testthat', 'covr', 'googledrive', 'curl', 'httpuv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'maptools', 'raster', 'readr', 'rgeos', 'ncdf4', 'pracma',
  'dygraphs', 'xts', 'maps', 'mapdata', 'oceanmap', 'sp', 'PBSmapping'

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:
  'Formula', 'maxLik', 'msm', 'plm', 'plotrix'

Packages suggested but not available for checking:
  'car', 'lmtest', 'memisc', 'pglm', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'hdrcde'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matlab', 'aspace', 'jpeg', 'dplyr', 'scales'

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:
  'knitr', 'testthat', 'tibble', 'rmarkdown', 'rworldmap'

VignetteBuilder 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', 'crul', 'fauxpas', '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:
  'dplyr', 'dbplyr', 'DBI', 'Rcpp', 'bit64'

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', 'magrittr', 'stringr', 'tibble', 'httr', 'lubridate',
  'rlang', 'tidyr', 'assertthat', 'tidyselect'

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', 'RCurl', 'XML', 'rjson', 'tm'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'pander', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat_p1.R'
Running the tests in 'tests/testthat_p1.R' failed.
Complete output:
  > #testing Randy Zwitch solution
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tcltk2', 'tkrplot', 'conclust', 'corrplot', 'e1071', 'factoextra',
  'FactoMineR', 'ggplot2', 'jpeg', 'mclust', 'mda', 'mmand', 'png',
  'randomForest', 'reshape', 'sp', 'stringi', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rJava'
cmaOptimDP: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Running examples in 'rCMA-Ex.R' failed
The error most likely occurred in:

> ### Name: cmaCalcFitness
> ### Title: Calculate the fitness of a population.
> ### Aliases: cmaCalcFitness
> 
> ### ** Examples
> 
> cma <- cmaNew();
Error in loadNamespace(x) : there is no package called 'rJava'
Calls: cmaNew ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'callr', 'cli', 'crayon', 'desc', 'digest', 'pkgbuild',
  'prettyunits', 'R6', 'rprojroot', 'sessioninfo', 'withr', 'xopen'

Packages suggested but not available for checking:
  'covr', 'knitr', 'mockery', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'sandwich', 'abind', 'colorspace', 'Hmisc', 'e1071', 'haven',
  'readstata13', 'readxl', 'nortest'

Package suggested but not available for checking: 'carData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcmdr'

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:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR', 'Rcmdr', 'gplots', 'viridis'

Packages suggested but not available for checking:
  'knitr', 'rqubic', 'BiocManager'

VignetteBuilder package required for checking but not installed: 'knitr'

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/GuideBiclustGUI.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crossdes', 'support.BWS', 'support.CEs', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'coin', 'multcomp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DCchoice', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'support.CEs', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'depthTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DoE.base', 'FrF2', 'DoE.wrapper', 'relimp', 'Rcmdr', 'RcmdrMisc'

Package suggested but not available for checking: 'FrF2.catlg128'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R2HTML', 'abind', 'ez', 'nortest', 'reshape', 'Rcmdr', 'RcmdrMisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'epiR', 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'EcoVirtual'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'xtable', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'readstata13'

Packages suggested but not available for checking:
  'abind', 'aod', 'aplpack', 'brant', 'car', 'clinfun', 'cmprsk',
  'lawstat', 'meta', 'metatest', 'netmeta', 'multcomp', 'mvtnorm',
  'Matching', 'pROC', 'survivalROC', 'survRM2', 'tableone', 'readxl',
  'lmerTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FactoMineR', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcmdr', 'doParallel', 'tcltk2', 'foreach', 'clue', 'ggplot2',
  'reshape2', 'tkrplot', 'iterators'

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: 'GWRM', 'RcmdrMisc', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'HH', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcmdr'

Packages suggested but not available for checking:
  'abind', 'car', 'distr', 'distrEx', 'e1071', 'effects', 'lmtest',
  'multcomp', 'qcc', 'relimp', 'RODBC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcmdr', 'ggplot2', 'ggthemes', 'plyr', 'RColorBrewer', 'scales',
  'tcltk2'

Packages suggested but not available for checking:
  'extrafont', '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: 'lfstat', 'Rcmdr'

Packages suggested but not available for checking: 'testthat', 'lmomRFA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'MAd', 'metafor'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'compute.es', 'ggplot2', 'gridExtra', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'ordinal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mixlm', 'pls', 'xtable', 'phia', 'Rcmdr', 'car'

Packages suggested but not available for checking:
  'lme4', 'leaps', 'mvtnorm', 'gmodels', 'abind', 'pbkrtest', 'vcd',
  'multcomp', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'orloca', 'orloca.es', 'Rcmdr'

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:
  'rrcov', 'tkrplot', 'Rcmdr', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'RColorBrewer'

Packages suggested but not available for checking:
  'YaleToolkit', 'qgraph', 'maps', 'ade4', 'effects', 'abind', 'vcd',
  'car', 'gpairs', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcmdr', 'demography', 'forecast', 'ftsa', 'ggplot2', 'dplyr',
  'scales', 'zoo', 'data.table'

Packages suggested but not available for checking: 'tkrplot', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcmdr', 'runjags', 'rmeta', 'igraph', 'coda', 'rjags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcmdr', 'ROCR', 'pROC', 'ResourceSelection'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lpSolve', 'sampling', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SCVA', 'SCRT', 'SCMA', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SLC', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sos', 'Rcmdr', 'tcltk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'steepness'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'date', 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcmdr', 'sutteForecastR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'TeachingDemos', 'Rcmdr'

Packages suggested but not available for checking: 'rgl', 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcmdr', 'Hmisc', 'tcltk2', 'randtests', 'tseries', 'IndexNumR',
  'lme4', 'distr', 'distrEx'

Package suggested but not available for checking: 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tm', 'NLP', 'slam', 'zoo', 'Rcmdr', 'tcltk2', 'ca', 'R2HTML',
  'RColorBrewer', 'latticeExtra', 'stringi'

Packages suggested but not available for checking:
  'SnowballC', 'ROpenOffice', 'RODBC', 'tm.plugin.factiva',
  'tm.plugin.lexisnexis', 'tm.plugin.europresse', 'tm.plugin.alceste',
  'twitteR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries', 'Rcmdr'

Packages suggested but not available for checking:
  'car', 'carData', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'WorldFlora', 'Rcmdr'

Packages suggested but not available for checking: 'data.table', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RcmdrMisc', 'car', 'effects', 'tcltk2', 'abind', 'relimp', 'lme4'

Packages suggested but not available for checking:
  'aplpack', 'colorspace', 'e1071', 'Hmisc', 'knitr', 'leaps',
  'lmtest', 'markdown', 'multcomp', 'nortest', 'readxl', 'rgl',
  'rmarkdown', 'sem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', '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: 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'rect'
display.brewer.all: no visible global function definition for 'text'
display.brewer.pal: no visible global function definition for 'image'
Undefined global functions or variables:
  image par rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
Package required but not available: 'magrittr'

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:
  'crul', 'tibble', 'jsonlite', 'data.table', 'glue'

Packages suggested but not available for checking: 'testthat', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DescTools', 'multcompView', 'plyr', 'EMT', 'coin', 'lmtest',
  'nortest'

Package suggested but not available for checking: 'FSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clisymbols', 'crayon', 'devtools', 'gert', 'gh', 'gtools',
  'rmarkdown', 'rstudioapi', 'stringr', 'usethis', 'xfun'

Packages suggested but not available for checking:
  'fs', 'knitr', 'remotes', 'testthat', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
addLine: no visible global function definition for 'abline'
ellipse: no visible global function definition for 'approx'
ellipse: no visible global function definition for 'tail'
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'diffr', 'ggplot2', 'httr', 'knitr', 'markdown',
  'microbenchmark', 'rmarkdown', 'rstudioapi', 'rvest', 'shiny',
  'shinythemes', 'testthat', 'xml2'

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:
  'crul', 'jsonlite', 'pdftools', 'hoardr'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'knitr', 'rmarkdown', 'rcrossref', 'vcr'

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: 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FITSio', 'Rcpp', 'mmap', 'tibble', 'rgl', 'cli', 'entropy', 'geoR',
  'nnls'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'R.rsp', 'gsl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'glmnet', 'fishMod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gmp', 'Rcpp', 'RcppThread'

Packages suggested but not available for checking:
  'testthat', 'numbers', 'microbenchmark', '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: 'Rcpp'

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:
  'knitr', 'rmarkdown', 'minidown'

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:
  'tinytest', 'pkgKitten', 'reticulate', 'slam'

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.
Packages required but not available: 'gmp', 'Rcpp', 'RcppThread'

Packages suggested but not available for checking:
  'testthat', 'numbers', 'RcppAlgos'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppClassic'

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

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:
  'knitr', 'rmarkdown', 'pinp', 'reticulate'

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', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Rcpp'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'inline', 'DEoptim'

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'

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: 'wrapr', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'tinytest', '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', 'functional', 'memoise', 'readr', 'Rdpack', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'inline', 'tinytest', 'pkgKitten', 'microbenchmark'

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.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'knitr'

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: 'Rcpp'

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LinkingTo' for 'Rcpp' is unused as it has no 'include' directory
Packages required but not available: 'data.table', 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: '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.
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.
Package required but not available: 'Rcpp'

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: 'Rcpp', 'RcppParallel', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'BH'

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:
  '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: 'Rcpp', 'nloptr'

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:
  'knitr', 'rmarkdown', 'prettydoc', 'mvtnorm', 'RcppEigen'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Rcpp', 'RUnit', 'knitr', 'rmarkdown'
Package unavailable to check Rd xrefs: 'Rcpp'
GNU make is a SystemRequirements.
Running 'doRUnit.R'
Running the tests in 'tests/doRUnit.R' failed.
Complete output:
  > stopifnot(require(RUnit, quietly = TRUE))
  Error: require(RUnit, quietly = TRUE) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'RUnit'
  Execution halted
Packages suggested but not available for checking:
  'RcppArmadillo', 'devtools', 'roxygen2', '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', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tinytest', 'inline', 'rbenchmark', 'pkgKitten'
Package unavailable to check Rd xrefs: 'inline'
Packages required but not available: 'Rcpp', 'RApiSerialize', 'BH'

Packages suggested but not available for checking:
  'RcppMsgPack', 'rredis', '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: 'zoo', '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: 'bit64', '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.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'minidown'

VignetteBuilder 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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'R.rsp', 'Rcpp'

VignetteBuilder package required for checking but not installed: 'R.rsp'
'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: '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: 'Rcpp'

Package suggested but not available for checking: 'tinytest'

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', 'uuid', 'microbenchmark'

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.
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: 'Rcpp', 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppGSL'

Packages suggested but not available for checking:
  'rbenchmark', 'microbenchmark', 'knitr', 'rmarkdown', 'pinp'

VignetteBuilder 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', 'data.table', 'foreach', 'doParallel', 'selectr',
  'webdriver', 'callr', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forecast', 'ggmap', 'htmltools', 'igraph', 'leaflet',
  'leafsync', 'lubridate', 'pals', 'raster', 'Rcpp', 'rgdal', '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.
Packages required but not available: 'RCurl', 'XML', 'httr', 'plyr'

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.
Package required but not available: 'truncnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'crul', 'xml2', 'plyr', 'dplyr', 'tibble', 'R6', 'shiny',
  'miniUI', 'stringr', 'DT'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'knitr', 'rmarkdown', 'vcr', 'bibtex'

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
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:
  'RcppAnnoy', 'igraph', 'mclust', 'NbClust', 'Rtsne', 'ggplot2',
  'pracma', 'umap', 'SingleCellExperiment'

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', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Rcssplot.Rnw'
(Is a VignetteBuilder field missing?)
'LazyData' is specified without a 'data' directory
Files named as vignettes but with no recognized vignette engine:
   'vignettes/Rcssplot.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available:
  'dplyr', 'purrr', 'glue', 'rlang', 'tidyr', 'stringr', 'pracma',
  'lfe', 'broom', 'forcats', 'magrittr', 'ggplot2', 'tidyselect'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', '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: 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bitops'

Package suggested but not available for checking: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'magrittr', 'tidyselect', 'tidyr', 'purrr',
  'rlang', 'stringr', 'ggplot2', 'Rdpack'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tcpl'

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: 'rjson'

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:
  'sf', 'curl', 'httr', 'jsonlite', 'magrittr'

Packages suggested but not available for checking:
  'raster', 'czso', 'units', 'ggplot2', 'stringr', 'rvest', 'xml2',
  'scales', 'knitr', 'testthat', 'roxygen2', 'devtools', 'rmarkdown',
  'dplyr', 'lwgeom', '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: 'knitr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', '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: 'roxygen2', 'xfun', 'formatR'

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'

Package suggested but not available for checking: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'vegan', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: '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: 'jsonlite', 'crul', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'webmockr', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'reticulate', 'semver'

Packages suggested but not available for checking:
  'testthat', 'DBI', 'devtools', 'RSQLite', 'RPostgreSQL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'data.table', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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:
  'Rcpp', 'minpack.lm', 'Rdpack', 'dplyr', 'magrittr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tibble', 'ggplot2', 'ggpubr'

VignetteBuilder 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', 'lpdensity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sandwich', 'lmtest', 'AER', 'Formula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'slam', 'truncreg', 'truncnorm', 'maxLik'

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', 'rlang'

Packages suggested but not available for checking:
  'covr', 'knitr', 'pander', 'rmarkdown', 'testthat', 'utf8'

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: 'clipr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'lintr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'segments'
drawkpc: no visible global function definition for 'lines'
modelimage: no visible binding for global variable 'topo.colors'
modelimage: no visible global function definition for 'filled.contour'
modelimage: no visible global function definition for 'title'
modelimage: no visible global function definition for 'axis'
modelimage: no visible global function definition for 'lines'
sincdata: no visible global function definition for 'runif'
sincdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  axis filled.contour lines rnorm runif segments terrain.colors title
  topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "segments",
             "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'R.methodsS3', 'R.oo', 'R.utils', 'base64enc'

Packages suggested but not available for checking:
  'digest', 'Cairo', '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:
  'redland', 'jsonld', 'stringi', 'readr', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'magrittr', 'covr', 'testthat', 'knitr', 'rmarkdown', 'jqr', 'DT',
  'tibble', 'purrr', 'lubridate', 'httr', 'xml2', 'jsonlite',
  'repurrrsive', 'nycflights13', '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:
  'httr', 'curl', 'plyr', 'XML', 'dplyr', 'xml2', 'readr',
  'data.table', 'purrr', 'lubridate'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'here'

VignetteBuilder 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', 'doParallel', 'foreach'

Packages suggested but not available for checking:
  'pryr', 'rARPACK', '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:
  'brio', 'R6', 'httr', 'jsonlite', 'magrittr', 'rappdirs', 'digest',
  'storr', 'xml2', 'qdapRegex', 'rgdal', 'getPass', 'haven', 'iotools'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'survey', 'data.table',
  'microbenchmark', 'sf'

VignetteBuilder 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', 'curl'

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'

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: 'descr'
sumry_categorical: no visible global function definition for 'freq'
sumry_continous: no visible global function definition for 'quantile'
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Running examples in 'RDIDQ-Ex.R' failed
The error most likely occurred in:

> ### Name: sumry_categorical
> ### Title: Summary of categorical variable
> ### Aliases: sumry_categorical
> 
> ### ** Examples
> 
> library(descr)
Error in library(descr) : there is no package called 'descr'
Execution halted
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RDieHarder/RDieHarder.Rcheck/00install.out' for details.
Packages required but not available:
  'CVXR', 'RANN', 'Rcpp', 'RcppDE', 'Rcsdp', 'Rdpack', 'RSpectra',
  'maotai', 'mclustcomp', 'RcppArmadillo', 'RcppDist'

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:
  'beanplot', 'gplots', 'pdist', 'stringr'

Packages suggested but not available for checking: 'knitr', 'ggplot2'

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', '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: 'binaryLogic', 'reshape2'

Packages suggested but not available for checking:
  'ape', 'testthat', 'knitr', 'rmarkdown', 'covr', 'vcfR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'AER', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'pipeR', 'readxl', 'rlist', 'R6',
  'stringr', 'xml2', 'lubridate'

Packages suggested but not available for checking:
  'chipPCR', 'magrittr', 'reshape2', 'qpcR', 'dplyr', 'ggplot2',
  'knitr', 'kfigr', 'MBmca', 'shiny', 'shinyjs', 'shinythemes',
  'shinyMolBio', 'V8', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rdrobust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'foreach', 'doParallel', 'RCurl',
  'org.Hs.eg.db'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'brew', 'httr', 'stringr', 'xml2'

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: 'R6', 'crayon', 'cli', 'prettycode'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'proto', '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:
  'urltools', 'glmnet', 'XML', 'httr', 'xml2', 'curl', 'virustotal',
  'aws.alexa', 'rlang', 'jsonlite', 'devtools'

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'

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', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rbibutils'

Packages suggested but not available for checking:
  'testthat', 'rstudioapi', 'rprojroot', 'gbRd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rdrobust'

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: 'rJava'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive', 'digest', 'dplyr', 'httr', 'jsonlite', 'magrittr',
  'purrr'

Packages suggested but not available for checking: 'testthat', 'uuid'

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:
  'crul', 'curl', 'tibble', 'hoardr', 'zip', 'jsonlite', 'mime'

Packages suggested but not available for checking: 'testthat', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'synchronicity' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages required but not available:
  'gridExtra', 'ggplot2', 'network', 'igraph', 'reshape2', 'scales',
  'anytime', 'Hmisc', 'statnet.common', 'ergm', 'isotone'

Packages suggested but not available for checking: 'survey', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'rjson', 'RCurl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCMCpack', 'mvtnorm', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'digest', 'gtools', 'jsonlite', 'knitr', 'provSummarizeR',
  'provViz', 'rlang', 'rmarkdown', 'sessioninfo', 'stringi', 'XML'

Packages suggested but not available for checking:
  'ggplot2', 'roxygen2', '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: 'ggplot2', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'serial'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'berryFunctions', 'pbapply'

Packages suggested but not available for checking:
  'RCurl', 'leaflet', 'knitr', 'rmarkdown', 'testthat', 'roxygen2',
  'devtools', 'remotes', 'bit64', 'data.table', 'OSMscale', 'raster',
  'R.utils', 'ncdf4', 'readr', 'dwdradar', 'XML', 'sp', 'rgdal'

VignetteBuilder 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', 'rgrass7'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reactable', 'dplyr', 'htmltools', 'shiny', 'stringr'

Package suggested but not available for checking: 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'htmltools', 'htmlwidgets', 'jsonlite', 'reactR'

Packages suggested but not available for checking:
  'covr', 'crosstalk', 'dplyr', 'leaflet', 'rmarkdown', 'shiny',
  'sparkline', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'jsonlite'

Packages suggested but not available for checking:
  'shiny', 'knitr', 'rmarkdown', 'htmltools', '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: 'rootSolve', 'deSolve', 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'htmltools'

Packages suggested but not available for checking:
  'htmlwidgets', 'rmarkdown', 'shiny', 'V8', 'knitr', 'usethis',
  'jsonlite'

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 required but not available:
  'readxl', 'dplyr', 'hutils', 'fst', 'curl', 'purrr', 'tidyr',
  'stringi', 'rsdmx', 'glue', 'httr', 'rvest', 'xml2', 'rlang'

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.
Packages required but not available: 'bmp', 'jpeg', 'png', 'tiff'

Packages suggested but not available for checking: 'pixmap', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'readMzXmlData', 'MALDIquantForeign'
Packages required but not available: 'plyr', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'raster', 'stringr', 'rgdal', 'rgeos', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'NCmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'R.utils'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'data.table', 'zoo', 'readr',
  'lubridate', 'zip'

VignetteBuilder 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', 'haven', 'jsonlite', 'readr', 'readxl'

Packages suggested but not available for checking:
  'devtools', 'dplyr', 'knitr', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'pinp'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'base64enc', 'digest', 'XML'

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', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'cellranger', 'readr', 'stringi'

Packages suggested but not available for checking:
  'dplyr', '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: 'xml2', 'rvest', 'purrr', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'tidyr', 'dplyr', 'purrr', 'rlang', 'xml2', 'rvest',
  'stringr', 'httr', 'lubridate'

Packages suggested but not available for checking:
  'covr', '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 required but not available: 'readr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'gdata'

VignetteBuilder 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', 'crayon', 'hms', 'rlang', 'R6', 'tibble',
  'lifecycle', 'BH', 'cpp11'

Packages suggested but not available for checking:
  'covr', 'curl', 'dplyr', 'knitr', 'rmarkdown', 'spelling', 'stringi',
  'testthat', '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: '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:
  'stringr', 'xml2', 'purrr', 'dplyr', 'rlang', 'stringi', 'magrittr',
  'deSolve'

Packages suggested but not available for checking:
  'testthat', 'igraph', 'knitr', 'rmarkdown', '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: '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: '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:
  'magrittr', 'tibble', 'purrr', 'readr', 'stringr', 'plyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'antiword', 'data.table', 'digest', 'httr', 'jsonlite', 'pdftools',
  'readODS', 'readxl', 'streamR', 'stringi', 'striprtf', 'tibble',
  'xml2'

Packages suggested but not available for checking:
  'knitr', 'pkgload', 'rmarkdown', 'quanteda', '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', 'curl'

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:
  'chk', 'hms', 'DBI', 'RSQLite', 'lifecycle', 'tibble'

Packages suggested but not available for checking:
  'covr', 'pool', 'testthat', 'knitr', 'rmarkdown', 'units', 'sf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cellranger', 'Rcpp', 'tibble', 'progress'

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: 'Rcpp', 'xml2', 'cellranger'

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: 'numDeriv', 'Rcpp', 'RcppArmadillo'

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:
  'checkmate', 'dplyr', 'lifecycle', 'plyr', 'purrr', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'plotly', 'testthat', 'tidyr', 'xpectr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'reliaR'

Packages suggested but not available for checking:
  'Rmosek', 'knitr', 'digest'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Bdecon.Rnw'
   'inst/doc/medde.Rnw'
   'inst/doc/rebayes.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'dplyr', 'assertthat'

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.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking:
  'flexmix', 'mclust', 'mixtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'stringi', 'testthat'
Packages unavailable to check Rd xrefs: 'stringi', 'rebus.unicode'
'LazyData' is specified without a 'data' directory
Running examples in 'rebus.base-Ex.R' failed
The error most likely occurred in:

> ### Name: Anchors
> ### Title: The start or end of a string.
> ### Aliases: Anchors START END exactly
> ### Keywords: datasets
> 
> ### ** Examples
> 
> START
<regex> ^
> END
<regex> $
> 
> # Usage
> x <- c("catfish", "tomcat", "cat")
> (rx_start <- START %R% "cat")
<regex> ^cat
> (rx_end <- "cat" %R% END)
<regex> cat$
> (rx_exact <- exactly("cat"))
<regex> ^cat$
> stringi::stri_detect_regex(x, rx_start)
Error in loadNamespace(x) : there is no package called 'stringi'
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
Package required but not available: 'rebus.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: 'rebus.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:
  'rebus.base', 'rebus.datetimes', 'rebus.numbers', 'rebus.unicode'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rebus.base'

Package suggested but not available for checking: 'stringi'

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
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'kriging', 'Rcpp'

Packages suggested but not available for checking:
  'devtools', 'dplyr', 'knitr', 'magrittr', 'rgl', '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: 'httr', 'RCurl', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ReCiPa: no visible global function definition for 'count.fields'
ReCiPa: no visible global function definition for 'read.table'
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'ellipsis', 'generics', 'glue', 'gower', 'ipred',
  'lifecycle', 'lubridate', 'magrittr', 'purrr', 'rlang', 'tibble',
  'tidyr', 'tidyselect', 'timeDate', 'withr'

Packages suggested but not available for checking:
  'covr', 'ddalpha', 'dimRed', 'fastICA', 'ggplot2', 'igraph',
  'kernlab', 'knitr', 'modeldata', 'RANN', 'RcppRoll', 'rmarkdown',
  'rsample', 'RSpectra', '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:
  'lvec', 'ldat', 'dplyr', 'stringdist', 'lpSolve', '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:
  'ape', 'vegan', 'picante', 'phangorn', 'phytools', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GA', 'Rcpp', 'sp'

Packages suggested but not available for checking:
  'doParallel', 'knitr', 'shiny', 'testthat', 'tufte', 'xtable'

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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crayon'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'recommenderlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'recommenderlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'arules', 'proxy', 'registry', 'irlba', 'recosystem'

Packages suggested but not available for checking: 'ROCR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rootSolve'

Packages suggested but not available for checking:
  'plot3D', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'rlang', 'survminer'

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', 'openssl'

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: 'data.table', 'crayon'

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', 'RSQLite', 'ff', 'e1071', 'ada', 'ipred', 'evd', 'data.table',
  'xtable'

Packages suggested but not available for checking: 'RUnit', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/BigData.rnw'
   'inst/doc/EVT.rnw'
   'inst/doc/Supervised.rnw'
   'inst/doc/WeightBased.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.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'ggpubr', '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', 'RcppProgress'

Packages suggested but not available for checking: 'knitr', 'prettydoc'

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', 'circular', 'prevR', 'scales', 'fields', 'move', 'knitr',
  'rmarkdown', 'sp', '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:
  'dplyr', 'magrittr', 'visNetwork', 'readr', 'shiny', 'shinyjs',
  'jsonlite', 'DT', 'colourpicker', 'rintrojs', 'markdown',
  'rstudioapi', 'crayon', '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:
  'Rcpp', 'ggplot2', 'splines2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tinytest'

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:
  'car', 'GPArotation', 'mclust', 'psych', 'UsingR', 'vcd'
Packages required but not available:
  'checkmate', 'chron', 'DBI', 'httr', 'labelVector', 'lubridate',
  'readr', 'stringr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'data.table', 'keyring', 'lubridate'

Packages suggested but not available for checking:
  'devtools', 'fs', 'knitr', 'magrittr', 'qwraps2', 'rmarkdown',
  'rjson', 'secret', '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:
  'checkmate', 'dplyr', 'httr', 'magrittr', 'readr', 'rlang', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'covr', 'DBI', 'kableExtra', 'knitr', 'odbc', 'rmarkdown',
  'sessioninfo', '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:
  'RJSONIO', 'igraph', 'magrittr', 'dplyr', 'visNetwork', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'snowfall', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'REddyProc'

Packages suggested but not available for checking:
  'ncdf4', 'RNetCDF', 'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rlang', 'mlegp', 'tibble', 'magrittr',
  'solartime', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'minpack.lm', 'segmented', 'knitr', 'rmarkdown',
  'lognorm', 'ggplot2', 'tidyr', 'bigleaf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.