Packages required but not available: 'glmnet', 'ncvreg', 'brglm2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'igraph', 'assertthat', 'expm', 'sets', 'purrr'

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

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

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

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

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

Package suggested but not available for checking: 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'raster'
Packages required but not available:
  'dplyr', 'magrittr', 'lubridate', 'PAutilities', 'rlang',
  'svDialogs', 'zoo'

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

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

Packages suggested but not available for checking:
  'sp', 'raster', 'rasterVis', 'tdr', 'meteoForecast'

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', 'knitr', 'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ranger', 'data.table', 'igraph', 'future.apply', 'R6', 'lgr'

Packages suggested but not available for checking:
  'tidyverse', 'uwot', 'mlbench', 'rsample'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'plyr', 'crul', 'xml2', 'jsonlite', 'tibble', 'R6'

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', 'dplyr', 'mime'

Packages suggested but not available for checking:
  'testthat', 'shiny', 'shinyjs', 'openssl'

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: 'reportr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'markdown', 'scatterplot3d', 'shiny', 'ggplot2',
  'ggwordcloud', 'metR', 'interp'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr', 'hexbin', 'shinycssloaders',
  'shinyBS', 'shinyjs', 'shinyjqui'

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.
bm: no visible global function definition for 'rnorm'
bm: no visible global function definition for 'ts'
fbm: no visible global function definition for 'fft'
fbm: no visible global function definition for 'rnorm'
fbm: no visible global function definition for 'ts'
gbm: no visible global function definition for 'rnorm'
gbm: no visible global function definition for 'ts'
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
getAlpha: no visible global function definition for 'pbinom'
kfweOrd: no visible global function definition for 'qnbinom'
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Packages required but not available:
  'rlist', 'kohonen', 'shiny', 'dplyr', 'plyr', 'openair',
  'colourpicker', 'shinycssloaders', 'shinycustomloader'

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

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'plyr', 'orthopolynom', '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: 'hexbin', 'kohonen', 'som'

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

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

Packages suggested but not available for checking:
  'reshape2', '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:
  'tuneR', 'seewave', 'ggplot2', 'jsonlite', 'mime', 'suncalc', 'hms'

Packages suggested but not available for checking:
  'av', 'testthat', 'covr', 'WaveletComp', 'devtools',
  'googleCloudStorageR', 'googleLanguageR', 'knitr', 'rmarkdown',
  'spelling'

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

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

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

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', 'ADGofTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'SpATS'
Running examples in 'SOP-Ex.R' failed
The error most likely occurred in:

> ### Name: rae
> ### Title: Defining random effects in SOP formula
> ### Aliases: rae
> ### Keywords: models smooth regression
> 
> ### ** Examples
> 
> library(SOP)
> require(SpATS)
Loading required package: SpATS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'SpATS'
> ## An example of use of SOP package for the analysis of field trials experiments.
> ## Taken from the SpATS package.
> data(wheatdata)
Warning in data(wheatdata) : data set 'wheatdata' not found
> 
> # Create factor variable for row and columns
> wheatdata$R <- as.factor(wheatdata$row)
Error in is.factor(x) : object 'wheatdata' not found
Calls: as.factor -> is.factor
Execution halted
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'magrittr'
Packages required but not available:
  'Rcpp', 'mathjaxr', 'Rdpack', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCMCpack', '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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'htmltools', 'htmlwidgets', 'learnr', 'shiny', 'assertthat',
  'jsonlite', 'ellipsis', 'rlang'

Packages suggested but not available for checking:
  'base64', 'knitr', 'testthat', 'withr', 'rmarkdown', 'magrittr',
  'webshot', 'spelling', '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:
  'Hmisc', 'pbapply', 'quantreg', 'SparseM'

Packages suggested but not available 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', 'RColorBrewer', 'dplyr', 'reshape2'

Packages suggested but not available for checking:
  'gdata', 'knitr', 'rmarkdown', 'RCurl', 'rjson', '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: 'brew'

Packages suggested but not available for checking: 'RODBC', 'WriteXLS'

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

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'knitr', 'testthat', 'roxygen2', 'markdown',
  'magrittr', 'kableExtra', 'rmarkdown', 'covr', 'ggrepel'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shinyBS', 'htmltools', 'seewave', 'DBI', 'dplyr', 'dbplyr',
  'RSQLite', 'signal', 'tuneR', 'zoo', 'magrittr', 'shinyFiles',
  'shiny', 'generics', 'keras', 'shinyjs'

Packages suggested but not available 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', 'shiny', 'shinyjqui'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'pracma', 'oce', 'ineq', 'vegan', 'tuneR', 'seewave'

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: 'SciencesPo', 'stringr'

Package which this enhances but not available for checking: 'RecordLinkage'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'shinyBS', 'tuneR', 'seewave', 'zoo', 'reshape2', 'mvtnorm', 'dtw',
  'phonTools', 'signal', 'shiny', 'shinyjs', 'foreach', '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:
  'abind', 'geomorph', 'plot3D', 'reshape2', 'seewave', 'tuneR'

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

Package suggested but not available for checking: 'flip'

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

Packages suggested but not available for checking:
  'knitr', 'rstan', 'DropletUtils', '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:
  'dplyr', 'tensorA', 'assertthat', 'Rcpp', 'gtools', 'R6', 'gplots',
  'SPIn', 'reshape2'

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:
  'gRbase', 'progress', 'reshape2', 'graph', 'igraph', 'gtools',
  'plyr', 'scales'

Packages suggested but not available for checking:
  'networkD3', 'ggplot2', 'Rgraphviz', 'knitr', 'rmarkdown',
  'r2cytoscape', 'BiocStyle', 'Biobase', 'graphite', 'hgu95av2.db',
  'ALL', 'mvtnorm', 'org.Hs.eg.db'

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
Packages required but not available:
  'broom', 'dplyr', 'future', 'furrr', 'ggplot2', 'gridExtra',
  'lmtest', 'lubridate', 'magrittr', 'mclust', 'purrr', 'randomForest',
  'sandwich', 'stringr', 'strucchange', 'tidyr', 'xts', 'zoo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'quantmod', '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:
  'NAM', 'lme4', 'reshape2', 'Rcpp', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'tibble', 'pbmcapply', 'purrr', 'rlist', 'XML', 'xml2',
  'DT', 'urltools'

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'

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'vegan'
Packages required but not available:
  'abind', 'dplyr', 'ggplot2', 'Rcpp', 'tidyr', '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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crsuggest', 'dplyr', 'ggraph', 'ggplot2', 'igraph', 'magrittr',
  'sf', 'spatstat.random', 'spatstat.geom', 'ggthemes'

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:
  'mclust', 'permute', 'RcppTN', 'Rfast', 'sna', 'vegan'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'rgl'
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'microbenchmark'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/isotherms.rnw'
(Is a VignetteBuilder field missing?)
Package unavailable to check Rd xrefs: 'colorSpec'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/isotherms.rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'sp', 'zoo', 'xts', 'intervals'

Packages suggested but not available for checking:
  'adehabitatLT', 'cshapes', 'gstat', 'maps', 'mapdata', 'maptools',
  'plm', 'raster', 'RColorBrewer', 'rgdal', 'rgeos', 'rmarkdown',
  'RPostgreSQL', 'knitr', 'googleVis', 'ISOcodes', 'markdown', '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', 'raster', 'rayshader', 'magrittr', 'png', 'jsonlite', 'rgdal'

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

VignetteBuilder 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', 'reticulate'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'quanteda', 'R.rsp', 'rmarkdown', 'spelling',
  'testthat', 'tidytext', 'tibble'

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: 'mapproj', 'RCEIM'

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

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

VignetteBuilder 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', 'magrittr', 'miniUI', 'reproducible', 'rstudioapi',
  'shiny', 'SpaDES.core', 'stringi'

Packages suggested but not available for checking:
  'covr', '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:
  'quickPlot', 'reproducible', 'crayon', 'data.table', 'fastdigest',
  'igraph', 'qs', 'raster', 'Require', 'whisker'

Packages suggested but not available for checking:
  'covr', 'DiagrammeR', 'dplyr', 'future', 'future.callr', 'ggplot2',
  'googledrive', 'httr', 'knitr', 'logging', 'magrittr', 'pkgload',
  'png', 'RandomFields', 'RColorBrewer', 'rgdal', 'roxygen2',
  'rstudioapi', 'sp', 'SpaDES.tools', '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:
  'quickPlot', 'reproducible', 'SpaDES.core', 'SpaDES.tools'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat', 'SpaDES.addins', 'spelling'

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:
  'backports', 'checkmate', 'CircStats', 'data.table', 'fastmatch',
  'fpCompare', 'magrittr', 'quickPlot', 'raster', 'Rcpp', 'Require',
  'rgeos', 'sp'

Packages suggested but not available for checking:
  'animation', 'bit', 'DBI', 'DEoptim', 'dplyr', 'dqrng', 'fasterize',
  'ff', 'ffbase', 'gdalUtils', 'googledrive', 'knitr', 'RandomFields',
  'RColorBrewer', 'rmarkdown', 'sf', 'testthat', 'covr'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'pomp', 'moments', 'earlywarnings'
'LazyData' is specified without a 'data' directory
Running examples in 'spaero-Ex.R' failed
The error most likely occurred in:

> ### Name: create_simulator
> ### Title: Create surveillance data simulator.
> ### Aliases: create_simulator
> 
> ### ** Examples
> 
> 
> foo <- create_simulator()
Error: The pomp package is needed for this function to work. Please install it.
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 suggested but not available for checking: 'spam'
Running examples in 'spam64-Ex.R' failed
The error most likely occurred in:

> ### Name: spam64-package
> ### Title: 64-bit extension for the SPArse Matrix Package spam
> ### Aliases: spam64-package spam64 SPAM64 Spam64
> ### Keywords: documentation package
> 
> ### ** Examples
> 
> library("spam")
Error in library("spam") : there is no package called 'spam'
Execution halted
Packages required but not available:
  'proxy', 'Rcpp', 'nloptr', 'minqa', 'pbapply', 'crayon', 'gmp',
  'ROI', 'geometry', 'RcppEigen'

Packages suggested but not available for checking:
  'maps', 'testthat', 'lme4', 'rsae', 'rcdd', 'pedigreemm', 'foreach',
  'future', 'future.apply', 'multilevel', 'Infusion', 'IsoriX',
  'blackbox', 'RSpectra', 'ROI.plugin.glpk', 'memoise', 'agridat'

Packages which this enhances but not available for checking:
  'multcomp', 'RLRsim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dotCall64'

Packages suggested but not available for checking:
  'spam64', 'fields', 'testthat', 'R.rsp', 'truncdist', 'knitr',
  'rmarkdown'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
hausman: no visible global function definition for 'pchisq'
span.formula: no visible global function definition for 'model.frame'
span.formula: no visible global function definition for 'model.matrix'
span.formula: no visible global function definition for
  'model.response'
spbe: no visible global function definition for 'cor'
spbe: no visible global function definition for 'pt'
spfe: no visible global function definition for 'cor'
spfe: no visible global function definition for 'pt'
sprandom: no visible global function definition for 'cor'
sprandom: no visible global function definition for 'pt'
summary.span: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
Packages required but not available: 'magrittr', 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'plyr', 'foreach', 'pracma', 'stringr', 'expm', 'signal',
  'minpack.lm', 'smoother', 'magrittr', 'ptw', 'mmand', 'RNifti',
  'RNiftyReg', 'fields', 'numDeriv', 'nloptr', 'irlba', 'jsonlite'

Packages suggested but not available for checking:
  'viridisLite', 'shiny', 'miniUI', 'knitr', 'rmarkdown', 'testthat',
  'ragg', '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: 'sparklyr', 'dplyr', 'DBI'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'dplyr'

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'formattable', '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: 'dbplyr', 'dplyr', 'rlang', 'sparklyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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:
  'sparklyr', 'jsonlite', 'listviewer', 'dplyr', 'rlang', 'purrr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("dbplyr"): there is no package called 'dbplyr'

See section 'Package namespaces' in the 'Writing R Extensions' manual.
Package required but not available: 'sparklyr'

Packages suggested but not available 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: 'sparklyr'

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: 'DBI', 'sparklyr', 'Rcpp'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
f.I2.cont: no visible global function definition for 'combn'
f.I2.dich: no visible global function definition for 'combn'
f.pstar.cont: no visible global function definition for 'combn'
f.pstar.dich: 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:
  'doFuture', 'doRNG', 'fields', 'foreach', 'future', 'iterators',
  'lifecycle', 'raster', 'sp', 'sparr', 'spatstat.geom',
  'spatstat.random'

Packages suggested but not available for checking:
  'spatstat.data', 'testthat', 'spelling', '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:
  'spatstat', 'spatstat.utils', 'spatstat.geom', 'spatstat.core',
  'spatstat.random', 'doParallel', 'foreach', 'misc3d'

Package suggested but not available for checking: 'fftwtools'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'bnlearn', 'graph', 'igraph', 'network', 'RCy3', 'testthat'
Packages unavailable to check Rd xrefs: 'RCy3', 'graph', 'igraph', 'network', 'bnlearn'
Unknown package 'sparsebn' in Rd xrefs
Running 'testthat.R'
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'
Packages required but not available:
  'bdsmatrix', 'corpcor', 'dplyr', 'ggplot2', 'mvtnorm', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'covr', 'modeldata', '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', '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:
  'directlabels', 'proto', 'ggplot2', 'Rcpp', 'VGAM', 'truncnorm',
  'RcppArmadillo'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RSpectra', 'assertthat', 'tidyr', 'ggplot2', 'magrittr', 'rlang',
  'dotCall64'

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

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', 'statmod', 'mvtnorm'
Malformed Description field: should contain one or more complete sentences.
Package unavailable to check Rd xrefs: 'mvtnorm'
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'numDeriv', 'scales', 'knitr', 'xtable', 'dplyr'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/sparseHessianFD.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:
  'bookdown', 'knitr', 'prettydoc', 'rmarkdown', 'R.rsp', 'xts'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown', 'R.rsp'
Running examples in 'sparseIndexTracking-Ex.R' failed
The error most likely occurred in:

> ### Name: spIndexTrack
> ### Title: Sparse Index Tracking
> ### Aliases: spIndexTrack
> 
> ### ** Examples
> 
> library(sparseIndexTracking)
> library(xts)
Error in library(xts) : there is no package called 'xts'
Execution halted
Packages required but not available: 'Rcpp', 'spam'

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: 'elasticnet', 'mda'

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

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

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: 'robustHD', 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: 'mvtnorm'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doRNG', 'foreach', '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:
  'Rcpp', 'future.apply', 'data.table', 'future', 'tidyverse',
  'lubridate', 'viridis', '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: 'lpSolve', 'Rcapture'

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:
  'dplyr', 'tidyr', 'ggplot2', 'forcats', 'mvtnorm', 'knitr',
  'bookdown', 'kableExtra', 'testthat', 'scales', 'trustOptim'

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: 'shape'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Rcpp'
Packages required but not available:
  'ggplot2', 'Rcpp', 'msm', 'VGAM', 'MCMCpack', 'coda', 'glmnet',
  'gridExtra', 'GIGrvg', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'glasso', 'longitudinal', 'huge', 'mvtnorm', 'network', 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ncvreg', 'doParallel', 'glmnet', 'ggplot2', 'reshape2', 'mvtnorm',
  'picasso', 'corpcor'

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', 'selectiveInference', 'glmnet', 'RcppArmadillo',
  'RcppEnsmallen'

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:
  'FactoMineR', 'dplyr', 'tidyr', 'ggplot2', 'plotly', 'stringr',
  'colorspace', 'crayon', 'shiny', 'shinydashboard', 'shinyjs',
  'shinyjqui', 'fpc', 'ggdendro', 'htmltools', 'rstudioapi',
  'htmlwidgets', 'shinythemes', 'markdown', 'explor', 'shinyWidgets',
  'scatterD3', 'sp', 'ks', 'rgdal', 'maptools', 'leaflet', 'ape',
  'mapview'

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

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

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BB', 'msm', 'numDeriv', 'plyr', '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.
Packages required but not available:
  'Rcpp', 'mvtnorm', 'multcomp', 'geepack'

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

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

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pracma', 'igraph', 'matrixStats', 'Rtsne', 'knitr', 'rmarkdown',
  'irlba'

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: 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'hexbin', 'ggplot2', 'lubridate', '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: 'Rcpp', 'JADE', 'sp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'sf', 'RandomFields', '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:
  'sp', 'sf', 'raster', 'spatstat.geom', 'spatstat.core', 'spdep',
  'rgeos'

Packages suggested but not available for checking:
  'exactextractr', 'readr', 'RCurl', 'RANN', 'rms', 'yaImpute',
  'SpatialPack', 'EnvStats', 'maptools', 'GeNetIt', 'gstat',
  'RStoolbox', 'terra', 'tabularaster', 'stringr'

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

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

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

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

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

Packages suggested but not available for checking:
  'INLA', 'geoR', 'SDraw', 'testthat', 'tmap', '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', 'rgeos', 'shape', 'sp', 'splancs'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ICSNP', 'MNM'
Packages unavailable to check Rd xrefs: 'ICSNP', 'MNM'
Package required but not available: 'fastmatrix'

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

Packages suggested but not available for checking:
  'lwgeom', 'doParallel', 'foreach', 'cartography', 'knitr',
  'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("spdep"): there is no package called 'spdep'

See section 'Package namespaces' in the 'Writing R Extensions' manual.
Packages required but not available: 'spdep', 'quantreg', 'GWmodel', 'plm'

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:
  'spData', 'sf', 'spdep', 'expm', 'coda', 'LearnBayes', 'gmodels'

Packages suggested but not available for checking:
  'RSpectra', 'tmap', 'spam', 'knitr', 'lmtest', 'sandwich',
  'rmarkdown', 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'magrittr', 'tibble', 'foreach', 'doParallel',
  'ranger', 'rlang', 'tidyr', 'tidyselect', 'huxtable', 'patchwork',
  'viridis'

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:
  'classInt', 'colourvalues', 'data.table', 'dplyr', 'fs', 'GenSA',
  'geohashTools', 'ggplot2', 'leafem', 'leafgl', 'leaflet',
  'lubridate', 'Rcpp', 'RcppProgress', 'sf', 'tmap', 'units', 'viridis'

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

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

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'modeldata', 'rmarkdown', 'tidyr', 'testthat',
  'yardstick', '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:
  'magrittr', 'dplyr', 'tidyr', 'ggplot2', 'scales', 'purrr', 'rlang',
  'plyr', 'spatstat.geom', 'spatstat.core', 'RColorBrewer', 'rlist',
  'furrr', 'future', 'tidyselect', 'crayon', 'pheatmap', 'ggpubr',
  'viridis'

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: 'spBayes', 'Rcpp', 'RcppArmadillo'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat', 'fields', 'smoothie', 'smatr', 'turboEM',
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'distillery',
  'maps', 'CircStats', 'fastcluster', 'waveslim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'future', 'Rcpp', 'ggplot2', 'plyr', 'future.apply', 'gsl',
  'segmented', 'RcppArmadillo'

Packages suggested but not available for checking:
  'moments', 'poweRlaw', 'reshape2', 'testthat', 'covr', 'acss',
  'gstat', 'sp', 'raster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'BH', 'colourvalues', 'geojsonsf', 'geometries', 'jsonify',
  'rapidjsonr', 'sfheaders'

Packages suggested but not available for checking:
  'colourvalues', 'covr', 'geojsonsf', 'jsonify', 'sfheaders', 'knitr',
  'rmarkdown', 'testthat'

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

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'asnipe', '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:
  'fields', 'plot3Drgl', 'spam', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.utils', 'spatstat.sparse', 'abind', 'tensor', 'goftest'

Packages suggested but not available for checking:
  'sm', 'maptools', 'gsl', 'locfit', 'RandomFields',
  'RandomFieldsUtils', 'fftwtools', 'nleqslv', 'spatstat.linnet',
  'spatstat'

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

Packages suggested but not available for checking:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet'

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

Packages suggested but not available for checking:
  'spatstat.core', 'spatstat.random', 'spatstat.linnet', 'maptools',
  'fftwtools', 'spatstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel',
  'spatstat.utils'

Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.data', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat',
  'spatstat.utils'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.data', 'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.utils', 'spatstat.sparse'

Packages suggested but not available for checking:
  'goftest', 'locfit', 'spatstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat', 'tensor',
  'spatstat.utils'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.core', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils', 'spatstat.linnet',
  'spatstat.core', 'spatstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat.data', 'spatstat.geom', 'spatstat.random', 'spatstat.core',
  'spatstat.linnet', 'spatstat.utils'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spatstat.core'
Package unavailable to check Rd xrefs: 'spatstat.core'
Packages required but not available:
  'sp', 'spatstat.core', 'spatstat.geom', 'spatstat.random',
  'spatstat', 'raster', 'iterators', 'RandomFields', 'fields',
  'stringr', 'rgeos', 'RColorBrewer', 'lubridate'

Packages suggested but not available for checking:
  'rgdal', 'rgl', 'OpenStreetMap'

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

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'maptools', 'raster', 'sf', 'rmarkdown',
  'knitr', 'covr', 'trip', '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: 'coda', 'sp', 'magic', 'Formula'

Packages suggested but not available for checking: 'MBA', 'geoR'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'LS2Wstat', 'gridExtra'

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'
Running 'testthat.R'
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', 'plyr'

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

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.
GenerateCliquesCovariance: 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:
  'msm', 'mvtnorm', 'Rcpp', 'RcppArmadillo'

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

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

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

Packages suggested but not available for checking:
  'maptools', 'rgdal', 'sf', 'spDataLarge', 'spdep', 'spatialreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rcarbon', 'data.table', 'dplyr', 'gdistance', 'ggplot2', 'raster',
  'smatr', 'viridisLite', 'magrittr', 'rlang', 'sp', 'gstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'spData', 'sf', 'deldir', 'units', 's2', 'e1071'

Packages suggested but not available for checking:
  'spatialreg', 'dbscan', 'rgeos', 'RColorBrewer', 'xtable',
  'maptools', 'igraph', 'RSpectra', 'knitr', 'rgdal', 'classInt',
  'tmap', 'spam', 'ggplot2', 'rmarkdown', 'tinytest', 'rgeoda'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("dplyr"): there is no package called 'dplyr'

See section 'Package namespaces' in the 'Writing R Extensions' manual.
Packages required but not available:
  'corpcor', 'forecast', 'plyr', 'Rcpp', 'separationplot', 'xtable',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'devtools', '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: 'raster', 'sp', 'deSolve', 'animation'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MassSpecWavelet', 'mQTL', 'doSNOW', 'data.table', 'foreach',
  'Rfast', 'ggplot2', 'gridExtra', 'reshape2', 'rvest', 'xml2',
  'missForest', 'impute'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
bartlett: no visible global function definition for 'pchisq'
local.rbfdot: no visible binding for global variable 'sd'
local.rbfdot: no visible global function definition for 'dist'
local.rbfdot : <anonymous>: no visible global function definition for
  'median'
speccalt: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
Package required but not available: 'abind'

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

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

Packages suggested but not available for checking:
  'imager', 'tidyverse', 'rgl', 'fftw', 'mrbsizeR', '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: 'xcms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'e1071', 'ggplot2', 'impute', 'ellipse', 'GGally', 'pcaPP',
  'compare', 'baseline', 'pls', 'readJDX', 'speaq', 'genefilter',
  'RColorBrewer', 'Metrics', 'imputeTS', 'specmine.datasets', 'mrbin',
  'plotly', 'narray'

Packages suggested but not available for checking:
  'ggdendro', 'reticulate', 'qdap', 'qpdf', 'scatterplot3d', 'MAIT',
  'xcms', 'KEGGgraph', 'KEGGREST', 'rcytoscapejs', 'rgl', 'curl',
  'RCurl', 'pins', 'knitr', 'rmarkdown'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cowplot', 'dplyr', 'ggplot2', 'ggraph', 'glue', 'igraph',
  'lme4', 'magrittr', 'purrr', 'rlang', 'tibble', 'tidyr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', '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:
  'ggplot2', 'plyr', 'reshape2', 'stringr', 'baseline', 'signal',
  'epiR'

Packages suggested but not available for checking:
  'caret', 'pls', 'RColorBrewer', 'knitr', 'rmarkdown', 'dplyr'

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

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

Packages suggested but not available for checking:
  'calendar', 'calendR', 'httptest', 'knitr', 'lubridate', 'lutz',
  'maps', 'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'magrittr', 'nnls', 'NMF', 'plotly', 'plyr', 'RColorBrewer',
  'signal', 'viridis', 'hNMF'

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', 'progress', 'rlist', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
  'CVXR', 'bookdown', 'knitr', 'prettydoc', 'rmarkdown', 'R.rsp',
  'testthat', 'patrick', 'corrplot', 'igraph', 'kernlab', 'pals',
  'clusterSim', 'viridis', 'quadprog', 'matrixcalc'

VignetteBuilder packages required for checking but not installed:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'scatterplot3d', 'fields'

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

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

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

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

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

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

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: 'data.table', 'foreach', 'lomb'

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

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

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:
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Packages unavailable to check Rd xrefs: 'beanplot', 'raster', 'plotrix'
Note: found 5 marked Latin-1 strings
Package required but not available: 'pooh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abjutils', 'dplyr', 'httr', 'janitor', 'lubridate', 'magrittr',
  'purrr', 'stringr', 'tidyr', 'xml2', 'rvest', 'rlang', 'tibble',
  'glue', 'httptest'

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', 'lubridate', 'magrittr', 'purrr', 'stringr', 'tibble', 'tm',
  'tidyr', 'pdftools', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'biglm'
Packages required but not available: 'dplyr', 'stringr', 'purrr'

Packages suggested but not available for checking: 'labelled', 'readroper'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BB', 'SQUAREM', 'ggplot2', 'sm', 'plyr', 'nleqslv'

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

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

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

Package suggested but not available for checking: 'pdftools'

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

Package suggested but not available for checking: 'gstat'

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

Package suggested but not available for checking: 'RColorBrewer'

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

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

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

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

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

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

Packages suggested but not available for checking: 'grpreg', 'refund'

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: 'coda', 'RSpectra', 'Rdpack'

Packages suggested but not available for checking:
  'covr', 'knitr', 'sf', 'sp', 'spdep', 'tinytest', 'rmarkdown'

VignetteBuilder 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', 'parallelMap', 'tictoc', 'ggplot2', 'mlbench'

Packages suggested but not available for checking:
  'caret', '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: 'pracma'

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

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

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'seqinr'
Package unavailable to check Rd xrefs: 'seqinr'
Packages required but not available: 'sp', 'spData'

Packages suggested but not available for checking:
  'spdep', 'maptools', 'rgdal'

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

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:
  'cubature', 'SimplicialCubature', 'mvmesh', 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatialreg', 'spdep', 'sp', 'mvtnorm', 'stringr', 'coda', 'spData',
  'sf'

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

Packages suggested but not available for checking:
  'CompQuadForm', 'dgof', 'goftest', 'knitr', 'markdown', 'mvtnorm',
  'numDeriv', 'progress', 'progressr', 'rmarkdown', 'scatterplot3d',
  'testthat', '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:
  'doParallel', 'foreach', 'stringr', 'tidyr', 'genlasso', 'purrr',
  'gplots'

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

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', 'robotstxt', 'tinytest'

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'akima', 'coda', 'ggplot2', 'gridExtra', 'MCMCpack', 'mvtnorm',
  'R2WinBUGS', 'reshape', 'scales'

Packages suggested but not available for checking:
  'mboost', 'mlbench', 'gtable'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gee', 'geepack', 'splancs', 'waveslim', 'rje', 'stringr', 'ggplot2',
  'RColorBrewer', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gridExtra', 'testthat', 'PresenceAbsence',
  'sp', '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:
  'tourr', 'ggplot2', 'gganimate', 'plotly', 'shiny', 'Rdimtools',
  'transformr', 'magrittr'

Packages suggested but not available for checking:
  'hexbin', 'htmlwidgets', 'gifski', 'png', 'dplyr', 'GGally',
  'rmarkdown', 'knitr', 'testthat', 'lifecycle', 'covr', '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: 'quadprog'

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

Packages suggested but not available for checking:
  'ComplexHeatmap', 'knitr', 'rmarkdown', 'grImport', 'grImport2',
  'jpeg', 'png', 'tiff', 'ape', 'cranlogs', 'cowplot', 'dendextend',
  'bezier', '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: 'xml2', 'httr', 'magrittr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gsheet', 'dplyr', 'reshape2', 'ggplot2', 'ggsci', 'readr',
  '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.
Package required but not available: 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'curl', 'httr', 'dplyr', 'purrr', 'stevedore', 'magick',
  'scales', 'formatR', 'openssl', 'stringi', 'HARtools', 'jsonlite',
  'lubridate'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'jpeg', 'png', '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:
  'Formula', 'maxLik', 'sphet', 'memisc', 'car', 'numDeriv'

Package suggested but not available for checking: 'spdep'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'RColorBrewer', 'actuar',
  'ChainLadder'

VignetteBuilder 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', '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:
  'mosaic', 'ggplot2', 'treeClust', 'mclust'

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

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

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', 'vctrs', 'mvnfast', 'glmnet'

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

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:
  'dplyr', 'tibble', 'psych', 'bcaboot', '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:
  'glmnet', 'latex2exp', 'RSpectra', 'ggplot2', '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: 'Rcpp', 'RcppArmadillo'

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', 'glmnet'

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

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

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

Package which this enhances but not available for checking: 'tree'
Package required but not available: 'data.table'

Packages suggested but not available for checking: 'covr', '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', 'ranger', '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', 'emulator', 'miscTools', 'penalized', 'ggplot2', 'gridExtra',
  'plot3D', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("spdep"): there is no package called 'spdep'

See section 'Package namespaces' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'
Package required but not available: 'pls'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.utils', 'neurobase', 'matlabr', 'oro.nifti', 'git2r'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kirby21.t1', 'kirby21.fmri', 'scales', '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:
  'spm', 'gstat', 'sp', 'randomForest', 'psy', 'gbm', 'ranger',
  'fields', 'glmnet', 'e1071'

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: 'sp', 'raster', 'rgeos'

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

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:
  'sp', 'fields', 'vegan', 'doParallel', 'foreach', 'ggplot2', 'spdep',
  'rARPACK', 'RColorBrewer', 'FNN'

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

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:
  'gstat', 'sp', 'randomForest', 'psy', 'gbm', 'biomod2', 'ranger'

Packages suggested but not available 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', 'rmarkdown', 'sf', 'spdep', 'tidyr', 'tmap'

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:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'spatstat',
  'leaflet', 'shiny', 'sp', 'raster', 'maptools', 'rgdal',
  'shinythemes', 'prodlim'

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: 'sp', 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spdep', 'maptools', 'rgeos', 'sp', 'raster', 'igraph', 'cubature',
  'future.apply', 'ggplot2', 'progressr', 'data.table', 'SearchTrees',
  'Rcpp', 'Rdpack', 'RcppProgress', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'future', 'testthat', 'knitr', 'kableExtra', 'rmarkdown',
  'RColorBrewer', 'classInt', 'reshape2', 'dplyr', 'rlang', 'rgdal',
  'rgl', 'tmap', 'FNN', 'smoothr', 'concaveman', '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: 'NMF'

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

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:
  'rgbif', 'rbison', 'rebird', 'rvertnet', 'ridigbio', 'lubridate',
  'crul', 'whisker', 'jsonlite', 'data.table', 'tibble', 'wellknown'

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

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

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

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

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'fortunes', 'ggplot2'
Packages unavailable to check Rd xrefs: 'fortunes', 'ggplot2'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Note that you would never run this file directly. This is used by tools::testInstallPackages()
  > # and other packages like covr.
  > # To actually run the tests, you need to set the working directory then run
  > # devtools::test()
  > 
  > # This line ensures that R CMD check can run tests.
  > # See https://github.com/hadley/testthat/issues/144
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(spongebob)
  > 
  > testthat::test_check('spongebob')
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'magrittr', 'ggplot2', 'jpeg', 'plyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
Packages required but not available: 'Rcpp', 'data.table', 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'lobstr', 'magrittr', 'pkgdown', 'rmarkdown',
  'spelling', '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: 'archetypes'
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.
fetch_NBAPlayerStatistics: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
Packages required but not available: 'CausalImpact', 'keras'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shinyBS', 'smoof', 'shiny', 'shinydashboard', 'SPOT', 'gridExtra',
  'shinyjs', 'rhandsontable', 'XML', 'rclipboard', 'plotly', 'httpuv',
  'shinyFiles', 'batchtools'

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: 'magrittr', 'dplyr', 'purrr', 'httr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'httr', 'lubridate', 'jsonlite', 'readr',
  'rvest', 'stringr', 'tibble', 'janitor', 'rlang', 'ggridges',
  'magrittr', 'genius', 'assertthat', '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:
  'benchmarkme', 'callr', 'emoa', 'ggsci', 'jsonlite', 'keras',
  'magrittr', 'mlr', 'OpenML', 'plotly', 'RColorBrewer', 'reticulate',
  'rpart.plot', 'sensitivity', 'smoof', 'SPOT', 'tensorflow',
  'tfdatasets'

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:
  'geodist', 'progress', 'dplyr', 'cli', 'patchwork', 'ggrepel',
  'ggExtra', 'ggbeeswarm', 'ggplot2'

Packages suggested but not available for checking:
  'sf', 'testthat', 'covr', '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:
  'DEoptim', 'ggplot2', 'glmnet', 'laGP', 'nloptr', 'plgp', 'plotly',
  'randomForest', 'ranger', 'rgenoud', 'rsm'

Packages suggested but not available for checking:
  'babsim.hospital', 'batchtools', 'car', 'farff', 'knitr',
  'microbenchmark', 'rmarkdown', 'OpenML', 'party', 'RColorBrewer',
  'readr', '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:
  'BalancedSampling', 'sampling', 'pracma', 'WaveSampling'

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:
  'broom', 'dplyr', 'ggplot2', 'gt', 'gtools', 'gridExtra', 'igraph',
  'magrittr', 'purrr', 'rsample', 'sp', 'spatialreg', 'spdep', 'sf',
  'tidyr', 'lwgeom', 'bookdown'

Packages suggested but not available 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', 'partitions', 'magic', 'mathjaxr', 'disordR'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'rgdal', 'rgeos', 'maptools'
Running examples in 'sp-Ex.R' failed
The error most likely occurred in:

> ### Name: disaggregate-methods
> ### Title: disaggregate SpatialLines, SpatialLinesDataFrame,
> ###   SpatialPolygons, or SpatialPolygonsDataFrame objects
> ### Aliases: disaggregate disaggregate-methods
> ###   disaggregate,SpatialPolygons-method
> ###   disaggregate,SpatialPolygonsDataFrame-method
> ###   disaggregate,SpatialLines-method
> ###   disaggregate,SpatialLinesDataFrame-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> Sr1 = Polygon(cbind(c(2,4,4,1,2),c(2,3,5,4,2)), hole = FALSE)
> Sr2 = Polygon(cbind(c(5,4,2,5),c(2,3,2,2)), hole = FALSE)
> Sr3 = Polygon(cbind(c(4,4,5,10,4),c(5,3,2,5,5)), hole = FALSE)
> Sr4 = Polygon(cbind(c(5,6,6,5,5),c(4,4,3,3,4)), hole = TRUE)
> 
> Srs1 = Polygons(list(Sr1, Sr2), "s1/2")
> Srs3 = Polygons(list(Sr3, Sr4), "s3/4")
> sp = SpatialPolygons(list(Srs1,Srs3), 1:2)
> length(sp) ## [1] 2
[1] 2
> length(disaggregate(sp)) ## [1] 3 
Error in explodePolygons(x, ...) : 
  package rgeos is needed to relate holes to their corresponding polygons
Calls: disaggregate -> disaggregate -> explodePolygons
Execution halted
Running 'agg.R'
Running the tests in 'tests/agg.R' failed.
Complete output:
  > options("rgdal_show_exportToProj4_warnings"="none")
  > library(sp)
  > g = SpatialGrid(GridTopology(c(5,5), c(10,10), c(3,3)))
  > p = as(g, "SpatialPolygons")
  > p$z = c(1,0,1,0,1,0,1,0,1)
  > cc = coordinates(g)
  > p$ag1 = aggregate(p, p, mean)[[1]]
  Error in over(by, x, fn = FUN, ...) : 
    package rgeos is required for additional over methods
  Calls: aggregate -> aggregate.Spatial -> over -> over
  Execution halted
Errors in running code in vignettes:
when running code in 'csdacm.Rnw'
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in 'intro_sp.Rnw'
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in 'over.Rnw'
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'csdacm.Rnw'... failed to complete the test
  'intro_sp.Rnw'... failed to complete the test
  'over.Rnw'... failed to complete the test
Packages required but not available:
  'Rcpp', 'assertthat', 'igraph', 'extrafont', 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'fs', 'gganimate', 'ggraph', 'gifski', '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: 'sn', 'ucminf'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidytext', 'dplyr', 'lubridate'
Note: found 199 marked UTF-8 strings
Running examples in 'spRingsteen-Ex.R' failed
The error most likely occurred in:

> ### Name: concerts
> ### Title: Metadata for concerts in the spRingsteen dataset.
> ### Aliases: concerts
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Packages required but not available: 'Rcpp', 'glmnet', '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:
  'ggplot2', 'cvTools', 'pcaPP', 'reshape2', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("utils", "head")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'testthis', 'dplyr', 'effsize'

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', 'mvtnorm', 'BayesLogit', 'truncnorm', 'igraph', 'MCMCpack',
  'patchwork', 'tidyr', 'dplyr', 'ggplot2', 'tidyselect', 'Seurat',
  'rlang', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'assertthat', 'stringr', 'glue', 'magrittr', 'shinytoastr',
  'shinyAce', 'htmltools', 'R6', 'crayon'

Packages suggested but not available for checking:
  'testthat', 'shinyjqui', 'spsUtil'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DEoptim', 'lhs', 'pracma', 'FME', 'hypergeo', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plot3D'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'Formula', 'ggplot2', 'gmodels', 'gridExtra', 'knitr',
  'lmtest', 'minqa', 'numDeriv', 'rlang', 'Rdpack', 'rmarkdown',
  'sparseMVN', 'spatialreg', 'spdep'

Packages suggested but not available for checking:
  'bookdown', 'dplyr', '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:
  'sf', 'survey', 'crossdes', 'deldir', 'lme4', 'sampling', 'units'

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

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

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

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

VignetteBuilder 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', 'assertthat', 'stringr', 'glue', 'magrittr', 'crayon', '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: 'spTimer', 'coda', 'sp', 'spacetime'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spam', 'fields', '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:
  'coda', 'sp', 'spacetime', 'extraDistr'

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

Packages suggested but not available for checking: 'RUnit', 'mvtnorm'

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

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', 'prettydoc', 'rgeos', 'tibble',
  'gstat'

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:
  'gstat', 'magrittr', 'mvtnorm', 'purrr', 'raster', 'sp', 'whisker'

Packages suggested but not available for checking:
  'dplyr', 'GGally', 'gridExtra', 'knitr', 'png', 'readr', '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:
  'e1071', 'edgeR', 'spatstat', 'spatstat.core', 'spatstat.geom',
  'spatstat.data', 'spatstat.sparse', 'spatstat.utils',
  'spatstat.linnet', 'viridis', 'ggplot2', 'reshape', 'imager',
  'infotheo', 'irlba', 'testthat', 'doSNOW', 'foreach'

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

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

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

Packages suggested but not available for checking:
  'RH2', 'RMySQL', 'RPostgreSQL', 'svUnit'

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

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

Package suggested but not available for checking: 'testthat'

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: 'rJava', 'rlang'

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

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

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

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

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

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

Packages which this enhances but not available for checking:
  'RPostgreSQL', 'RODBC', 'RMySQL', 'RSQLite', 'RJDBC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mclust', 'nor1mix'

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: 'glmnet', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'setRNG'
Running examples in 'SQUAREM-Ex.R' failed
The error most likely occurred in:

> ### Name: fpiter
> ### Title: Fixed-Point Iteration Scheme
> ### Aliases: fpiter
> 
> ### ** Examples
> 
> 
> ##############################################################################
> # Example 1:  EM algorithm for Poisson mixture estimation 
> poissmix.em <- function(p,y) {
+ # The fixed point mapping giving a single E and M step of the EM algorithm
+ # 
+ pnew <- rep(NA,3)
+ i <- 0:(length(y)-1)
+ zi <- p[1]*exp(-p[2])*p[2]^i / (p[1]*exp(-p[2])*p[2]^i + (1 - p[1])*exp(-p[3])*p[3]^i)
+ pnew[1] <- sum(y*zi)/sum(y)
+ pnew[2] <- sum(y*i*zi)/sum(y*zi)
+ pnew[3] <- sum(y*i*(1-zi))/sum(y*(1-zi))
+ p <- pnew
+ return(pnew)
+ }
> 
> poissmix.loglik <- function(p,y) {
+ # Objective function whose local minimum is a fixed point \
+ # negative log-likelihood of binary poisson mixture
+ i <- 0:(length(y)-1)
+ loglik <- y*log(p[1]*exp(-p[2])*p[2]^i/exp(lgamma(i+1)) + 
+ 		(1 - p[1])*exp(-p[3])*p[3]^i/exp(lgamma(i+1)))
+ return ( -sum(loglik) )
+ }
> 
> # Real data from Hasselblad (JASA 1969)
> poissmix.dat <- data.frame(death=0:9, freq=c(162,267,271,185,111,61,27,8,3,1))
> y <- poissmix.dat$freq
> tol <- 1.e-08
> 
> # Use a preset seed so the example is reproducible. 
> require("setRNG")
Loading required package: setRNG
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'setRNG'
> old.seed <- setRNG(list(kind="Mersenne-Twister", normal.kind="Inversion",
+     seed=54321))
Error in setRNG(list(kind = "Mersenne-Twister", normal.kind = "Inversion",  : 
  could not find function "setRNG"
Execution halted
Running 'Hasselblad1969.R'
Running the tests in 'tests/Hasselblad1969.R' failed.
Complete output:
  > require("SQUAREM")  # master funcion and the 4 different SQUAREM algorithms
  Loading required package: SQUAREM
  > require("setRNG")   # needed to reproduce the same results
  Loading required package: setRNG
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'setRNG'
  > 
  > # data for Poisson mixture estimation  from Hasselblad (JASA 1969)
  > poissmix.dat <- data.frame(death=0:9, freq=c(162,267,271,185,111,61,27,8,3,1))
  > 
  > y <- poissmix.dat$freq
  > tol <- 1.e-08
  > 
  > # generate a random initial guess for 3 parameters
  > setRNG(list(kind="Wichmann-Hill", normal.kind="Box-Muller", seed=123))
  Error in setRNG(list(kind = "Wichmann-Hill", normal.kind = "Box-Muller",  : 
    could not find function "setRNG"
  Execution halted
Errors in running code in vignettes:
when running code in 'SQUAREM.Rnw'

> library("SQUAREM")

> help(package = SQUAREM)

> require("setRNG")
Loading required package: setRNG
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'setRNG'

> setRNG(list(kind = "Wichmann-Hill", normal.kind = "Box-Muller", 
+     seed = 123))

  When sourcing 'SQUAREM.R':
Error: could not find function "setRNG"
Execution halted

  'SQUAREM.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'SQUAREM.Rnw' using Sweave
Loading required package: setRNG
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'setRNG'

Error: processing vignette 'SQUAREM.Rnw' failed with diagnostics:
 chunk 3 (label = rng) 
Error in setRNG(list(kind = "Wichmann-Hill", normal.kind = "Box-Muller",  : 
  could not find function "setRNG"

--- failed re-building 'SQUAREM.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'plyr', 'tibble', 'lubridate', 'stringr', 'tidyr', 'rvest',
  'polite', 'naniar', 'janitor', 'Hmisc', 'rlang'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyMatrix', 'ggplot2', 'plotly', 'lme4', 'arm',
  'data.table', 'brms'

Package suggested but not available for checking: 'testthat'

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

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

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

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

VignetteBuilder package required for checking but not installed: 'R.rsp'
Packages unavailable to check Rd xrefs: 'RColorBrewer', 'colorspace'
Packages required but not available:
  'doParallel', 'elasticnet', 'foreach', 'mvtnorm'

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

Package suggested but not available for checking: 'survey'

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

Packages which this enhances but not available for checking:
  'amen', 'TripleR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DESeq2', 'futile.logger', 'ggplot2', 'ggsci', 'plyr', 'VennDiagram'

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:
  'vegan', 'shiny', 'DT', 'shinycssloaders', 'shinybusy'

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

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

Packages suggested but not available for checking:
  'convey', 'DBI', 'dbplyr', 'ggplot2', 'knitr', 'laeken', 'rmarkdown',
  'pander', '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:
  'foreach', 'r4ss', 'gtools', 'ggplot2', 'bbmle'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tsBSS', 'ICtest', 'JADE', 'BSSprep', 'ggplot2', 'xts', 'zoo'

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

Package suggested but not available for checking: 'testthat'

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

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

Packages suggested but not available for checking:
  'caret', 'e1071', 'C50', 'kernlab', 'testthat', 'timeDate',
  'stringi', 'R.rsp'

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

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

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:
  'psych', 'TTR', 'MAd', 'metafor', 'SingleCaseES'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'bigstatsr', 'chickn', 'RcppParallel', 'glmnet', 'foreach',
  'doParallel', 'doRNG', 'reshape2', 'pracma', 'Rdpack',
  'RcppArmadillo', 'rmio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'raster', 'earth', 'gbm', 'randomForest', 'dismo', 'e1071',
  'ggplot2', 'reshape2', 'scales', 'shiny', 'shinydashboard',
  'shinyFiles', 'spThin', 'poibin'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ssd : correction_method_D: no visible global function definition for
  'rnorm'
ssd : generate_bootstrap: no visible global function definition for
  'rmultinom'
ssd : bootstrap_method: no visible global function definition for
  'median'
ssd : bootstrap_method: no visible global function definition for
  'quantile'
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for 'rmultinom'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'median'
ssd : unbalanced_bootstrap_method: no visible global function
  definition for 'quantile'
ssd: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'chk', 'fitdistrplus', 'abind', 'actuar', 'ggplot2', 'lifecycle',
  'tibble', 'scales', 'VGAM', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat', 'readr', 'rlang', 'purrr',
  'tidyr', 'dplyr', 'R.rsp', 'mle.tools', 'reshape2'

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

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: 'pwr', 'MESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("spdep"): there is no package called 'spdep'

See section 'Package namespaces' 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: 'BDgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'stringr', 'gtools', 'BIGDAWG', 'gmt', 'DescTools',
  'dplyr', 'filesstrings'

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

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

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Biobase', 'edgeR', 'limma', 'qvalue', 'ssize.fdr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'parsnip', 'plyr', 'dplyr', 'magrittr', 'purrr', 'rlang', 'proxy',
  'generics', 'RANN', 'foreach', 'RSSL', 'conclust', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'caret', 'tidymodels', 'e1071', 'C50', 'kernlab', 'testthat',
  'doParallel', 'tidyverse', 'factoextra', 'covr', 'kknn',
  'randomForest', 'ranger', 'knitr', 'rmarkdown'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'CircStats', 'dtw', 'ggplot2',
  'cowplot', 'BH', 'RcppEigen', 'StanHeaders'

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: 'sampleSelection', 'robustbase'

Package suggested but not available for checking: 'mvtnorm'

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

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

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:
  'RSQLite', 'sp', 'igraph', 'maptools', 'rgdal', 'rgeos', 'BH'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
map.world: no visible global function definition for 'par'
map.world: no visible global function definition for 'plot.new'
map.world: no visible global function definition for 'plot.window'
map.world: no visible global function definition for 'lines'
map.world: no visible global function definition for 'title'
map.world: no visible global function definition for 'axis'
map.world: no visible global function definition for 'box'
plot.smooth.sspline: no visible global function definition for
  'predict'
plot.smooth.sspline: no visible global function definition for
  'filled.contour'
plot.smooth.sspline: no visible binding for global variable
  'terrain.colors'
plot.smooth.sspline: no visible global function definition for 'title'
plot.smooth.sspline: no visible global function definition for 'axis'
station: no visible binding for global variable 'WTdiff'
station: no visible global function definition for 'points'
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Packages required but not available: 'vegan', 'sampling', 'ggplot2'

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 required but not available: 'RDS', 'scam', 'coda'

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

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

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

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

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: 'survRM2'

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

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

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

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

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

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

VignetteBuilder 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', 'e1071', 'ggplot2', 'VGAM'

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

Package suggested but not available for checking: 'maps'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
error.est : <anonymous>: no visible global function definition for
  'median'
holm.robust: no visible global function definition for 'pnorm'
holm.robust: no visible global function definition for 'median'
holm.robust: no visible global function definition for 'mad'
huberize: no visible global function definition for 'quantile'
ssvd.initial: no visible global function definition for 'mad'
ssvd.iter.thresh: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
Packages required but not available:
  'bayestestR', 'BoomSpikeSlab', 'checkmate', 'ggplot2', 'rlang'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GIGrvg', 'numDeriv', 'normalp', 'Formula', 'sandwich'

Packages suggested but not available for checking: 'NISTnls', 'gam', 'sn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'dplyr', 'bigstep', 'rsample', 'tibble', 'purrr', 'tidyr',
  'stringr', 'ggplot2', 'broom', 'caret', 'ncvreg', 'knitr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfortify', 'lme4', 'magrittr', 'matrixStats',
  'reshape2', 'rlang', 'scales', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'glmnet', 'corpcor', 'ggplot2', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'fBasics', 'FMStable', 'RUnit', 'Rmpfr', 'sfsmisc'
Packages unavailable to check Rd xrefs: 'FMStable', 'fBasics'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'stabledist', 'testthat', 'numDeriv', 'xtable', 'fBasics'

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

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

Packages suggested but not available for checking:
  'Formula', 'evtree', 'rchallenge', '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: 'rmutil'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggm', 'matrixcalc', 'sem', 'nsga2R', 'graph', 'Rgraphviz',
  'polycor', 'foreach'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'cowplot', 'ggdendro', 'ggplot2', 'igraph', 'knitr', 'mlbench',
  'rmarkdown', 'testthat'

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'mboost'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'sandwich', 'zoo', 'mice', 'dplyr', '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 unavailable to check Rd xrefs: 'pryr', 'functional', 'dplyr', 'ks', 'purrr', 'data.table'
Packages required but not available:
  'tune', 'dplyr', 'rlang', 'tibble', 'purrr', 'parsnip', 'workflows',
  'recipes', 'rsample', 'workflowsets', 'butcher', 'yardstick',
  'tidyr', 'dials', 'glue', 'ggplot2', 'glmnet', 'cli', 'foreach',
  'generics'

Packages suggested but not available for checking:
  'testthat', 'covr', 'kernlab', 'knitr', 'modeldata', 'rmarkdown',
  'ranger', 'kknn'

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

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

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', 'bnlearn', 'covr', 'clue', 'igraph'
Running 'testthat.R'
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: 'deSolve', 'PBSddesolve'

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', 'reshape2', 'purrr', 'Rcpp', 'magrittr', 'tidyr', 'coop',
  'RcppEigen'

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

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

Package suggested but not available for checking: 'igraph'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
find.names: no visible global function definition for 'na.omit'
generate.names: no visible global function definition for 'na.omit'
standardize.countrynames: no visible global function definition for
  'data'
standardize.names: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages required but not available:
  'httr', 'curl', 'jsonlite', 'fst', 'data.table'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'loo', 'RcppParallel', 'Rcpp', 'rstan', 'rstantools', 'tidyverse',
  'dplyr', 'tibble', 'httr', 'bridgesampling', 'tidyselect',
  'latex2exp', 'tidyr', 'ggplot2', 'ggfan', 'BH', 'RcppEigen',
  'StanHeaders'

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', '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:
  'stringr', 'assertthat', 'glue', 'XML', 'rJava'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'geoTS', 'foreach', 'trend', 'doParallel', 'iterators',
  'mapview', 'RColorBrewer', 'rgdal'

Package suggested but not available for checking: 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'eemR', 'dplyr', 'tidyr', 'stringr', 'pracma', 'zoo',
  'tibble', 'multiway', 'GGally', 'doParallel', 'drc', 'foreach',
  'data.table', 'matrixStats', 'MBA', 'cdom', 'R.matlab', 'readr',
  'gtools', 'viridisLite'

Packages suggested but not available for checking:
  'plotly', 'xlsx', 'knitr', 'kableExtra', 'askpass', 'httr',
  '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:
  'AER', 'betareg', 'brglm', 'censReg', 'dynlm', 'eha', 'erer', 'ergm',
  'fGarch', 'gee', 'glmx', 'gmm', 'lfe', 'lme4', 'lmtest', 'mclogit',
  'mlogit', 'ordinal', 'plm', 'pscl', 'quantreg', 'rms', 'relevent',
  'robustbase', 'sampleSelection', 'spdep', 'survey'
Packages required but not available:
  'Rcpp', 'ggplot2', 'scales', 'RcppArmadillo'

Package suggested but not available for checking: 'spdep'

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'

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'estima.Rnw'
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'estima.Rnw' using 'UTF-8'... failed to complete the test
Packages required but not available: 'glmnet', 'cornet'

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

Packages which this enhances but not available for checking:
  'CVXR', '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: 'R2HTML', 'gss'

Packages suggested but not available for checking:
  'HiddenMarkov', 'snow', 'rstream'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'tibble', 'tidyr', 'tidyselect', 'snakecase',
  'purrr', 'rlang', 'pander', 'generics'

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: 'sf', 'stars', 'nngeo', 'units'

Packages suggested but not available for checking:
  'tinytest', 'knitr', 'rmarkdown', '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:
  'abind', 'sf', 'classInt', 'lwgeom', 'rlang', 'units'

Packages suggested but not available for checking:
  'PCICt', 'RNetCDF', 'clue', 'covr', 'cubelyr', 'digest', 'dplyr',
  'exactextractr', 'future.apply', 'ggforce', 'ggplot2', 'ggthemes',
  'gstat', 'httr', 'jsonlite', 'knitr', 'maps', 'mapdata', 'ncdfgeom',
  'ncmeta', 'pbapply', 'plm', 'randomForest', 'raster', 'rgdal',
  'rmarkdown', 'sp', 'spacetime', 'spatstat', 'spatstat.geom',
  'starsdata', 'terra', 'testthat', 'tidyr', 'viridis', 'xts', 'zoo'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'leaflet', 'plumber', 'png', 'rlang', 'sf', 'stars', 'units',
  'assertthat'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet.extras', 'webshot', 'mapview',
  'callr', 'magick', 'shiny', 'dplyr', 'magrittr', 'abind', 'testthat',
  'withr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fs', 'gert', 'glue', 'here', 'purrr', 'R.utils', 'readr',
  'renv', 'rlang', 'stringr', 'tibble', 'usethis'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'bigmemory', 'future', 'multiApply', 'easyNCDF', 's2dv',
  'ClimProjDiags', 'PCICt'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'commonmark'
Error(s) in re-building vignettes:
--- re-building 'startup-intro.md' using selfonly
Error: processing vignette 'startup-intro.md' failed with diagnostics:
there is no package called 'commonmark'
--- failed re-building 'startup-intro.md'

SUMMARY: processing the following file failed:
  'startup-intro.md'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ks', 'zoo', 'doSNOW', 'foreach', 'matrixcalc', 'optimParallel',
  'vars', 'xts', 'lessR', 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'ggplot2', 'tibble', 'rlang', 'tidyr',
  'patchwork', 'purrr', 'readr', 'stringr', 'yaml', 'lpSolve',
  'gtools', 'data.tree', 'RColorBrewer', 'zoo', 'Rcpp', 'arrow', 'BH'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'psycho', 'dplyr', 'corrgram', 'Hmisc',
  'rpivotTable', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'tidyselect', 'dplyr', 'ggplot2', 'lazyeval',
  'matrixStats', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'lubridate', '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: 'tibble', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'EnvStats', 'BSDA', 'purrr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sgeostat', 'e1071', 'MBA', 'rgl', 'robustbase', 'xtable', 'sp',
  'geoR'

Package suggested but not available for checking: 'mclust'

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

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

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

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

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

VignetteBuilder 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', 'lifecycle'

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

Packages suggested but not available for checking:
  'extraDistr', 'invgamma', 'matrixStats', 'VGAM'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'officer', '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:
  'emmeans', 'ggplot2', 'gridExtra', 'knitr', 'lme4', 'statgenSTA',
  'xtable'

Packages suggested but not available for checking:
  'asreml', '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:
  'animation', 'factoextra', 'ggforce', 'ggplot2', 'ggnewscale',
  'gridExtra', 'locfit', 'lubridate', 'reshape2', 'scales', 'SpATS'

Packages suggested but not available for checking:
  'asreml', '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: 'ggplot2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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:
  'statgenGWAS', 'data.table', 'ggplot2', 'gridExtra', 'LMMsolver',
  'scales', 'statgenIBD'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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:
  'emmeans', 'ggplot2', 'ggrepel', 'gridExtra', 'knitr', 'lme4',
  'mapproj', 'maps', 'qtl', 'scales', 'SpATS', 'xtable'

Packages suggested but not available for checking:
  'asreml', '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:
  'igraph', 'rARPACK', 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'downloader', 'lubridate', 'lutz', 'progress',
  'stringr', 'tidyr', '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: 'kutils', 'rmarkdown', 'knitr'

Packages suggested but not available for checking:
  'rockchalk', 'xtable', 'lavaan', 'psych', '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: 'clue'

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: 'omnibus', 'rlist'

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

Packages suggested but not available for checking:
  'Hmisc', 'mipfp', 'clue', 'RANN'

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 suggested but not available for checking: 'tweedie'
Package unavailable to check Rd xrefs: 'tweedie'
Package required but not available: 'coda'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tergm', 'ergm.count', 'sna', 'tsna', 'ergm', 'network',
  'networkDynamic', 'statnet.common'

Packages suggested but not available for checking:
  'ergm.rank', 'ergm.ego', 'EpiModel', 'degreenet', 'latentnet',
  'networksis', 'relevent', 'ndtv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'ergm', 'network', 'latticeExtra', 'sna', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'dplyr', 'httr', 'jsonlite', 'lifecycle', 'lubridate',
  'magrittr', 'purrr', 'readr', 'rlang', 'stringi', 'stringr',
  'tibble', 'tidyr', 'tidyselect', 'usethis', 'xml2'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'ragg', '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: 'mathjaxr', '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: 'stringr', 'tidytext', 'wordcloud'

Packages suggested but not available 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: 'truncdist', 'plyr', 'ggplot2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'psycho', 'dplyr', 'corrgram', 'Hmisc',
  'rpivotTable', 'psych'

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

Packages suggested but not available for checking:
  'curl', 'dplyr', 'ggplot2', 'knitr', 'lubridate', 'rmarkdown',
  'stringr', 'testthat', 'tidyr', 'pkgdown', 'kableExtra', 'leaflet',
  'geojsonsf', 'htmltools', 'tmap', 'jsonlite', 'pct', 'spatstat.core',
  'spatstat.geom', 'spatstat', 'osmdata', '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:
  'glue', 'httr', 'jsonlite', 'purrr', 'tidyr', 'tibble', 'stringr',
  'lubridate'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BayesFactor', 'correlation', 'datawizard', 'dplyr', 'effectsize',
  'glue', 'insight', 'magrittr', 'parameters', 'performance', 'rlang',
  'tibble', 'tidyr', 'WRS2', 'zeallot'

Packages suggested but not available for checking:
  'afex', 'ggplot2', 'knitr', 'metaBMA', 'metafor', 'metaplus',
  'purrr', 'rmarkdown', 'spelling', 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'data.table', 'readr', 'shinydisconnect',
  'knitr', 'kableExtra', 'car', 'DDoutlier', 'energy', 'corrplot',
  'ggplot2', 'gridExtra', 'reshape2'

Packages suggested but not available for checking:
  'nortest', 'lmtest', 'DescTools', 'psych', 'Hmisc',
  'PerformanceAnalytics', 'reticulate', 'fastDummies', 'semTools',
  'semPlot', 'FactoMineR', 'FactoInvestigate', 'factoextra', 'rrcov',
  'imputeMissings', 'onewaytests'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'httr', 'curl', '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:
  'Biobase', 'ggplot2', 'GGally', 'dplyr', 'reshape2', 'ggdendro',
  'tibble', 'ggfortify', 'ggrepel', 'gbm', 'forestplot', 'rpart.plot',
  'gridExtra', 'pROC', 'factoextra', 'pvca', 'limma', 'randomForest',
  'glmnet', 'knitr', 'rmarkdown', 'pheatmap', 'RColorBrewer',
  'tidyverse', '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: 'VCA'

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

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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'data.table', 'numDeriv', 'drgee'

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', 'clue', 'combinat'

Packages suggested but not available for checking:
  'irlba', 'JADE', 'ProDenICA', 'fastICA', 'energy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
Package required but not available: 'igraph'

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', '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.
Packages required but not available:
  'Rcpp', 'mvtnorm', 'tmvtnorm', 'MCMCglmm', 'ggplot2', 'distances',
  'Rdpack', '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: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'devtools', 'lintr', 'pkgdown', 'rhub', 'roxygen2',
  'spelling', '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: 'glue', 'betareg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gtools', 'FD', 'vcd', 'ade4', 'geometry', 'ape'

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: 'pracma'

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

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

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

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

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

VignetteBuilder 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', 'mvtnorm', 'pROC', 'dfoptim', 'caret'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spm', 'randomForest', 'spm2', 'psy'

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

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

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

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', 'SplitGLM', 'nnls', 'RcppArmadillo'

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:
  'Rcpp', 'raster', 'future', 'future.apply', 'rasterVis',
  'viridisLite', 'memuse'

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

VignetteBuilder 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: 'foreach', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bezier', 'rjson', 'shiny', 'Rcpp', 'jpeg', 'tiff', 'png', 'svgViewR'

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:
  'knitr', 'rmarkdown', 'tibble', '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: 'crayon', 'curl', 'jsonlite', 'yaml'

Packages suggested but not available for checking:
  'knitr', 'openssl', 'redux', 'reticulate', 'rmarkdown', 'testthat',
  'withr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'magrittr', 'labelled', 'arm', 'purrr', 'tibble', 'dplyr',
  'lme4', 'rlang', 'forcats', 'stringr', 'httr', 'rmarkdown', 'tidyr',
  'bib2df'

Packages suggested but not available for checking:
  'knitr', 'DBI', 'RSQLite', 'dbplyr'

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.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'abind', 'fda', 'raster',
  'rasterVis', 'RColorBrewer'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'e1071'

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', 'brnn', 'kernlab', 'randomForest', 'rrBLUP'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'readr', 'readxl', 'rlang', 'rvest',
  'sf', 'stringr', 'tibble', 'xml2'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'mapview', '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: 'forecast', 'nnfor'

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

Package suggested but not available for checking: 'plot3D'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maptools', 'reshape2', 'sp', 'spacetime', 'zoo', 'nabor', 'gstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stm', 'markdown', 'shinyjs', 'shinythemes', 'tm', 'shiny', 'shinyBS'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stm', 'tidygraph', 'ggraph', 'igraph', 'ggrepel', 'shiny',
  'shinyBS', 'shinydashboard', 'shinyjs', 'ggplot2', 'purrr',
  'stringr', 'dplyr', 'tibble', 'readr', 'huge', 'scales'

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

VignetteBuilder 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', 'forecast', 'rootSolve', 'fanplot', 'reshape2', 'fields',
  'RColorBrewer'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'data.table', 'glmnet', 'lda', 'matrixStats', 'quadprog',
  'quanteda', 'slam', 'stringr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'clue', 'geometry', 'huge', 'igraph', 'LDAvis', 'NLP', 'rsvd',
  'Rtsne', 'SnowballC', 'spelling', 'testthat', 'tm', 'wordcloud'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggstance', 'magrittr', 'quantreg', '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:
  'truncnorm', 'coda', 'fields', 'rARPACK'

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: 'Rcpp', 'coda', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'mvtnorm', '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/article2.Rnw'
(Is a VignetteBuilder field missing?)

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rbenchmark', 'quantmod', 'dvmisc', 'Hmisc', 'lubridate',
  'RColorBrewer', 'Rcpp', 'TTR', 'zoo'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spray', 'permutations', 'partitions', 'mathjaxr', 'disordR'

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

VignetteBuilder 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', 'glmnet'

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

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

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

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

Packages suggested but not available for checking:
  'DBI', 'RSQLite', 'RPostgres', 'knitr', 'mockr', 'progress',
  'rbenchmark', '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:
  'cli', 'crayon', 'dplyr', 'fansi', 'httr', 'lifecycle', 'purrr',
  'R6', 'rappdirs', 'readr', 'rlang', 'stringr', 'tibble', 'tidyjson',
  'tidyr'

Packages suggested but not available for checking:
  'covr', 'curl', 'isa2', 'jsonlite', 'knitr', 'progress', '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', 'httr', 'jsonlite', 'tibble', 'urltools'

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:
  'AlgDesign', 'scales', 'scatterplot3d', 'emoa'

Packages suggested but not available for checking:
  'R.rsp', 'EMMREML', 'quadprog', 'UsingR', 'glmnet', 'leaps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'curl', 'dplyr', 'httr', 'jsonlite', 'stringr', 'maptools',
  'raster', 'rgeos', 'geosphere', 'Rcpp', 'nabor', 'rlang', 'lwgeom',
  'sf', 'magrittr', 'sfheaders', 'data.table', 'pbapply',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'igraph', 'rmarkdown', 'dodgr', 'cyclestreets',
  'leaflet', 'rgdal', 'pct', 'tmap', 'openxlsx', 'osrm', 'geodist',
  'mapsapi', 'opentripplanner'

VignetteBuilder 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', 'sas7bdat', 'nloptr', '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:
  'rpanel', 'splancs', 'ggplot2', 'gridExtra', 'plot3D', 'rgl',
  'spatstat.core', 'spatstat.geom', 'spatstat.random'

Packages suggested but not available 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:
  'splancs', 'dplyr', 'tidyr', 'magrittr', 'sf', 'rgdal', 'sp', 'ks',
  'terra', 'raster', 'SiMRiv', 'data.table', 'tibble', 'stringr',
  'lubridate', 'spatstat.geom', 'sparr', 'chron', 'ggplot2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'Rglpk', 'dplyr', 'tidyr', 'arrow', 'lubridate', 'rlang',
  'yaml', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'shiny', 'shinyFiles', 'shinyjs',
  'DT', 'Rsymphony', 'officer', 'flextable', '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: 'ape', 'geoscale'

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

Packages suggested but not available for checking:
  'knitr', 'optmatch', 'rmarkdown', 'testthat', 'glmnet',
  '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: 'Rglpk', 'snowfall', 'stratification'

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: 'zoo', 'xts'

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', 'RcppArmadillo'

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

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

Packages suggested but not available for checking:
  'knitr', 'StrathE2E2examples', '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: 'bnlearn', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'partykit', 'ranger', 'glmnet', 'ggplot2', 'ggparty',
  'mvtnorm', 'coin'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'BART', 'pROC', 'survRM2', 'TH.data',
  'sandwich', 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'C50', 'dplyr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'BalancedSampling', 'testthat',
  'StatMatch', 'laeken', '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:
  'fitdistrplus', 'zipfR', 'actuar', 'triangle', 'mc2d'

Packages suggested but not available 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', 'dplyr', 'stringr', 'shiny', 'diagram', 'reshape'

Packages suggested but not available for checking:
  'astrochron', 'RFOC', 'tidyverse', 'plyr'

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

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

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

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:
  'FNN', 'ggplot2', 'colorspace', 'pcaPP', 'ks'

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

Packages suggested but not available for checking: 'limma', 'samr'

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dismo', 'raster', 'deldir', 'rgeos',
  'ggplot2', 'reshape2', '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: 'zoo', 'chron', 'maptools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'registry', 'proxy', 'clue', 'clusterGeneration', 'dbscan', 'fpc',
  'mlbench', 'Rcpp', 'BH'

Packages suggested but not available for checking:
  'animation', 'DBI', 'rJava', 'RSQLite', 'testthat'

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

Package suggested but not available for checking: 'ROAuth'

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

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', 'XML', 'latticeExtra'

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', 'checkmate', 'magrittr', 'rlang', 'stringi'

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

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

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

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

VignetteBuilder 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: 'tibble'

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

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

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

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

Packages suggested but not available for checking:
  'qs', 'knitr', 'rmarkdown', 'usethis', 'dplyr', 'stringr', 'rlang'

VignetteBuilder 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.
Found the following significant warnings:
  icu69/common/cstring.h:43:70: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 156 bytes from a string of length 156 [-Wstringop-truncation]
See 'C:/r_packages/pkgcheck/CRAN/stringi/stringi.Rcheck/00install.out' for details.
Packages required but not available: 'glue', 'magrittr', 'stringi'

Packages suggested but not available for checking:
  'covr', 'htmltools', 'htmlwidgets', '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: 'stringi'

Package suggested but not available for checking: 'realtest'

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

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

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

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

Package suggested but not available for checking: 'STRaitRazoR'

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

Packages suggested but not available for checking:
  'spdep', 'rgeos', 'sf', 'Ecdat', 'tidycensus', 'ggplot2',
  'patchwork', 'gt', 'markdown'

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:
  'aod', 'broom', 'car', 'ggplot2', 'lme4', 'lmerTest', 'lsmeans',
  'mutoss', 'pbkrtest', 'phia', 'survey'

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

Packages suggested but not available for checking:
  'testthat', 'demography', 'knitr', 'rmarkdown', 'doParallel',
  'seasonal', '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: 'zoo', 'sandwich'

Packages suggested but not available for checking:
  'car', 'dynlm', 'e1071', 'foreach', 'lmtest', 'mvtnorm', 'tseries'

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

Packages suggested but not available for checking:
  'car', 'dynlm', 'e1071', 'foreach', 'lmtest', 'mvtnorm', 'tseries',
  'bfast'

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

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

VignetteBuilder 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', 'penalized'

Packages suggested but not available 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: 'matrixcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gWidgets2', 'gridExtra', 'gtable', 'plyr', 'scales',
  'data.table'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'lavaan', 'MplusAutomation'
Package unavailable to check Rd xrefs: 'lavaan'
Running examples in 'stuart-Ex.R' failed
The error most likely occurred in:

> ### Name: bruteforce
> ### Title: Subtest construction using a brute-force approach
> ### Aliases: bruteforce
> 
> ### ** Examples
> 
> 
> # Bruteforce selection in a minimal example
> # selecting 3 of 5 items
> # requires lavaan
> data(fairplayer)
> fs <- list(ra = names(fairplayer)[53:57])
> sel <- bruteforce(fairplayer, fs, 3,
+   cores = 1)  # number of cores set to 1
Loading required namespace: lavaan
Failed with error:  'there is no package called 'lavaan''
Error: lavaan is not installed. You could try or Mplus instead.
Execution halted
Package required but not available: 'testthat'

Packages suggested but not available for checking:
  'mockr', 'rmarkdown', 'knitr', '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:
  'purrr', 'readr', 'tidyr', 'dplyr', 'jsonlite', 'tibble', 'R.utils',
  'skimr', 'visdat', 'ggplot2', 'crayon'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'tidyverse', 'pls', 'nnls', 'CCA', 'MatrixCorrelation',
  '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:
  'ADGofTest', 'numDeriv', 'MCMCpack', 'matlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'crayon'
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:
  'cli', 'magrittr', 'purrr', 'R.cache', 'rematch2', 'rlang',
  'rprojroot', 'tibble', 'withr'

Packages suggested but not available for checking:
  'data.tree', 'digest', 'dplyr', 'here', 'knitr', 'prettycode',
  'rmarkdown', 'roxygen2', 'rstudioapi', '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: 'corpus'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', '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:
  'tcltk2', 'ape', 'pamr', 'e1071', 'tsne'

Packages suggested but not available for checking:
  'stringi', 'networkD3', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr', '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:
  'alluvial', 'circlize', 'colorspace', 'diagram', 'dplyr', 'ggplot2',
  'ggrepel', 'gridBase', 'gridExtra', 'plyr', 'polyclip', 'scales',
  'shape', 'sp', 'survRM2', 'UpSetR', 'VennDiagram'

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'subgxe-Ex.R' failed
The error most likely occurred in:

> ### Name: pasta
> ### Title: pasta for multi-phenotype analysis
> ### Aliases: pasta
> 
> ### ** Examples
> 
> # grab synthetic study for example
> data("studies")
> n.studies <- 5
> study.sizes <- c(nrow(studies[[1]]), nrow(studies[[2]]), nrow(studies[[3]]),
+                    nrow(studies[[4]]), nrow(studies[[5]]))
> study.pvals <- rep(0, n.studies)
> # Correlations of p-values among the studies.
> # In this case the studies were generated independently so its just I
> cor.matrix <- diag(1, n.studies)
> # load the lrtest() function to conduct the likelihood ratio test
> # Used just to generate the input p-values, not required in pasta itself.
> 
> library(lmtest)
Error in library(lmtest) : there is no package called 'lmtest'
Execution halted
Packages required but not available: 'mvtnorm', 'sensitivityfull'

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

Packages suggested but not available for checking:
  'adegraphics', 'ape', 'CircStats', 'deldir', 'maptools', 'pixmap',
  'spdep', 'splancs', 'waveslim'

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

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

Package suggested but not available for checking: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'CTT', 'irtoys', 'sirt', 'ltm', 'cocor'

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

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

Packages suggested but not available for checking:
  'arm', 'caret', 'cvAUC', 'e1071', 'earth', 'gam', 'gbm', 'glmnet',
  'Hmisc', 'ipred', 'LogicReg', 'mda', 'mlbench', 'party', 'polspline',
  'quadprog', 'randomForest', 'SIS', 'spls', 'stepPlr'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BiocGenerics', 'GSVA', 'igraph', 'pheatmap', 'rvest', 'xml2',
  'ChemmineR'

Packages suggested but not available 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: 'penalized', 'ROCR'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'magrittr', 'rlang', 'stringr', 'ggplot2',
  'psych', 'readr', 'tidyr', 'ggrepel', 'patchwork', 'forcats',
  'naniar', 'scales'

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

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

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

Packages suggested but not available for checking:
  'sudoku', '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: 'tkrplot'
'library' or 'require' call to 'tkrplot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "segments", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize uniroot
Consider adding
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'geosphere', 'lwgeom', 'progress', 'purrr', 'rlang',
  'rmapshaper', 'sf', 'tibble', 'tidyr', 'utf8'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'pkgdown', 'rmarkdown', 'spData', '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', 'dplyr', 'gtable', 'lubridate', 'rlang'

Packages suggested but not available for checking:
  'covr', 'knitr', 'plotly', 'readr', 'rmarkdown', 'testthat', 'tidyr',
  'tsibble', '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: 'seqminer', 'GBJ'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'checkmate', 'dplyr', 'htmltools', 'lubridate',
  'magick', 'matrixStats', 'pander', 'pryr', 'rapportools', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'forcats', 'formatR', 'kableExtra', 'knitr', 'magrittr', 'rmarkdown',
  '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:
  'survey', 'spdep', 'ggplot2', 'scales', 'reshape2', 'viridis', 'sp',
  'shadowtext', 'ggridges', 'data.table', 'RColorBrewer'

Packages suggested but not available for checking:
  'INLA', 'knitr', 'rmarkdown', 'readstata13', 'patchwork', 'rdhs',
  'R.rsp', 'fields'

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: 'matrixStats'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'd3r', 'dplyr', 'htmlwidgets', 'htmltools'

Packages suggested but not available for checking:
  'jsonlite', 'knitr', 'markdown', 'pipeR', 'testthat', 'tidyr',
  'rmarkdown'

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

VignetteBuilder 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', 'lubridate', 'magrittr'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'data.table', 'dplyr', 'RCurl', 'jsonlite', 'raster', 'purrr',
  'measurements', 'RANN', 'cartogram', 'fasterize', 'packcircles',
  'rmapshaper', 'sp', 'spdep', 'Rcpp', 'httr', 'rlang', 'automap'

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

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.
Malformed Description field: should contain one or more complete sentences.
sunter: 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: 'mvtnorm', 'gtools'

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:
  'amap', 'knitr', 'rmarkdown', 'fields', 'dbscan'

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: 'biclust', 'fabia'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'psych', 'plyr', 'ggplot2', 'lsr', 'Rdpack', 'shiny', 'shinyBS',
  'stringr'

Packages suggested but not available for checking:
  'emojifont', 'fMultivar', 'gridExtra', 'knitr', 'lawstat', 'car',
  'png', 'reshape2', 'rmarkdown', 'sadists', 'scales', '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:
  'sf', 'terra', 'philentropy', 'future.apply', 'cpp11'

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

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: 'coda'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'R6', 'Rcpp', 'fftw', 'RcppEigen'

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

VignetteBuilder 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', 'gtable', 'magrittr', 'plyr', 'scales',
  'ggdendro'

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

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

Packages suggested but not available for checking:
  'arm', 'bartMachine', 'biglasso', 'bigmemory', 'caret', 'devtools',
  'e1071', 'earth', 'extraTrees', 'gbm', 'genefilter', 'ggplot2',
  'glmnet', 'ipred', 'KernelKnn', 'kernlab', 'knitr', 'LogicReg',
  'mlbench', 'nloptr', 'party', 'polspline', 'prettydoc', 'quadprog',
  'randomForest', 'ranger', 'RhpcBLASctl', 'ROCR', 'rmarkdown', 'SIS',
  'speedglm', 'spls', 'sva', 'testthat', 'xgboost'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
TrainSuperMDS: no visible global function definition for 'rnorm'
TrainSuperMDSOnce: no visible global function definition for 'cmdscale'
TrainSuperMDSOnce: no visible global function definition for 'quantile'
distmat: no visible global function definition for 'dist'
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Packages required but not available: 'mice', 'SuperLearner'

Packages suggested but not available for checking:
  'arm', 'bartMachine', 'e1071', 'earth', 'extraTrees', 'gbm',
  'glmnet', 'ipred', 'KernelKnn', 'kernlab', 'LogicReg', 'party',
  'polspline', 'randomForest', 'ranger', 'speedglm', 'spls', 'xgboost'

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

Packages suggested but not available for checking:
  'knitr', 'rlang', 'testthat', 'rmarkdown', 'naivebayes', 'ClusterR',
  'FNN', 'ranger', 'caret', 'xgboost', 'glmnet', 'e1071'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'cli', 'magrittr', 'purrr', 'rlang', 'stringr',
  'vctrs', 'pillar', 'backports', 'lifecycle', 'withr'

Packages suggested but not available for checking:
  'car', 'covr', 'lintr', 'lme4', 'testthat', 'vdiffr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RSpectra', 'psych', 'fBasics', 'R.matlab', 'glmnet', 'matrixStats',
  'timeSeries', 'matlabr', 'spls', 'pracma', 'matlab'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'afex', 'emmeans', 'ggplot2', 'gridExtra', 'reshape2',
  'dplyr', 'magrittr', 'tidyselect', 'Hmisc', 'tidyr'

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

VignetteBuilder 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', 'prodlim'

Package suggested but not available for checking: 'testthat'

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

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

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

Package suggested but not available for checking: 'testthat'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RcppZiggurat'
Package unavailable to check Rd xrefs: 'RcppZiggurat'
Package suggested but not available for checking: 'DoE.base'
Package unavailable to check Rd xrefs: 'DoE.base'
Packages suggested but not available for checking:
  'crossdes', 'DoE.base', 'support.CEs'
Packages unavailable to check Rd xrefs: 'support.CEs', 'DoE.base', 'crossdes'
Running examples in 'support.BWS3-Ex.R' failed
The error most likely occurred in:

> ### Name: bws3.dataset
> ### Title: Creating a dataset suitable for Case 3 best-worst scaling
> ###   analysis
> ### Aliases: bws3.dataset
> ### Keywords: manip
> 
> ### ** Examples
> 
> # The following lines of code construct choice sets for Case 3 BWS
> # using rotation.design() in the package support.CEs; create a dataset
> # for the analysis using bws3.dataset(); and then conduct a maxdiff model
> # analysis on the basis of a conditional logit model specification
> # using clogit() in the package survival.
> 
> # Load packages
> library(support.CEs)
Error in library(support.CEs) : there is no package called 'support.CEs'
Execution halted
Packages suggested but not available for checking:
  'DoE.base', 'crossdes', 'mlogit', 'gmnl', 'apollo'
Packages unavailable to check Rd xrefs: 'mlogit', 'gmnl', 'apollo', 'DoE.base', 'crossdes'
Running examples in 'support.BWS-Ex.R' failed
The error most likely occurred in:

> ### Name: ricebws1
> ### Title: Consumers' preferences for rice characteristics
> ### Aliases: ricebws1
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # Respondents were asked to select their most and least important
> # characteristics of rice when purchasing rice. Rice characteristics
> # were assumed to be place of origin, variety, price, taste, safety,
> # wash-free rice, and milling date. BWS questions were created from
> # a balanced incomplete block design (BIBD) with seven treatments
> # (items), four columns (four items per question), and seven rows
> # (seven questions).
> 
> # Generate the BIBD using find.BIB() in the crossdes package:
> require("crossdes")
Loading required package: crossdes
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'crossdes'
> set.seed(8041)
> bibd.ricebws1 <- find.BIB(trt = 7, b = 7, k = 4)
Error in find.BIB(trt = 7, b = 7, k = 4) : 
  could not find function "find.BIB"
Execution halted
Packages required but not available: 'DoE.base', 'simex'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pROC', 'glmnet', 'MAP', 'Rcpp', 'foreach', 'doParallel',
  '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: 'ggplot2', 'goftest', 'gridExtra'

Packages suggested but not available for checking:
  'ordinal', 'rms', 'testthat', 'VGAM'

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

Package suggested but not available for checking: 'igraph'

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

Package suggested but not available for checking: 'roxygen2'

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

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

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

Packages suggested but not available for checking:
  'foreach', 'doParallel', '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: 'learnr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'latticeExtra', 'lme4', 'msm', 'OrdinalLogisticBiplot', 'logistf',
  'rms', 'mixtools', 'ks', 'rootSolve', 'extraDistr', 'pbapply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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:
  'optimx', 'copula', 'eha', 'lme4', 'msm', 'mvmeta', 'optextras',
  'parfm', 'SurvCorr'

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

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: 'rms'
Malformed Title field: should not end in a period.
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.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines predict survfit
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Running examples in 'survAUC-Ex.R' failed
The error most likely occurred in:

> ### Name: schemper
> ### Title: Distance-based estimator of survival predictive accuracy
> ###   proposed by Schemper and Henderson
> ### Aliases: schemper
> ### Keywords: classif
> 
> ### ** Examples
> 
> 
> library(rms)
Error in library(rms) : there is no package called 'rms'
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BiocParallel'
Package required but not available: 'fields'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'cubature', 'mvtnorm', 'simex'

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

Packages suggested but not available for checking:
  'gridExtra', 'colorspace', 'scales', 'animation', 'msm', 'spc',
  'quadprog', 'memoise', 'polyclip', 'rgeos', 'gpclib', 'maptools',
  'intervals', 'spdep', 'numDeriv', 'maxLik', 'gsl', 'fanplot',
  'hhh4contacts', 'tinytest', 'coda', 'splancs', 'gamlss', 'INLA',
  'runjags', 'MGLM', 'knitr'

Packages which this enhances but not available for checking:
  'xts', 'ggplot2'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/hhh4_spacetime.Rnw'
   'inst/doc/twinSIR.Rnw'
   'inst/doc/twinstim.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstantools', 'Rcpp', 'RcppParallel', 'rstan', 'tidybayes', 'dplyr',
  'rlang', 'tidyr', 'ggplot2', 'gridExtra', 'scales', 'ggdist', 'BH',
  'RcppEigen', 'StanHeaders'

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: 'Iso', 'nloptr', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AER: no visible binding for global variable 'survexp.fr'
AER: no visible global function definition for 'na.omit'
AER: no visible global function definition for 'survexp'
AER: no visible global function definition for 'poisson'
AER: no visible global function definition for 'glm'
AER: no visible global function definition for 'qnorm'
LR: no visible binding for global variable 'survexp.fr'
LR: no visible global function definition for 'na.omit'
LR: no visible global function definition for 'survexp'
LR: no visible global function definition for 'pchisq'
SMR: no visible binding for global variable 'survexp.fr'
SMR: no visible global function definition for 'na.omit'
SMR: no visible global function definition for 'survexp'
SMR: no visible global function definition for 'qnorm'
SMR: no visible global function definition for 'pchisq'
SMR: no visible global function definition for 'glm'
SMR: no visible binding for global variable 'poisson'
survexp_plot: no visible binding for global variable 'survexp.fr'
survexp_plot: no visible global function definition for 'na.omit'
survexp_plot: no visible global function definition for 'par'
survexp_plot: no visible global function definition for 'survfit'
survexp_plot: no visible global function definition for 'survexp'
survexp_plot: no visible global function definition for 'lines'
survexp_plot: no visible global function definition for 'legend'
survexp_plot: no visible global function definition for 'curve'
survexp_plot: no visible global function definition for 'arrows'
survexp_plot: no visible global function definition for 'points'
Undefined global functions or variables:
  arrows curve glm legend lines na.omit par pchisq points poisson qnorm
  survexp survexp.fr survfit
Consider adding
  importFrom("graphics", "arrows", "curve", "legend", "lines", "par",
             "points")
  importFrom("stats", "glm", "na.omit", "pchisq", "poisson", "qnorm")
to your NAMESPACE file.
Packages required but not available:
  'plyr', 'dplyr', 'functional', 'stringr', 'Rcpp', 'RcppArmadillo'

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: 'survey', 'magrittr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'gridExtra', 'ISLR', 'knitr', 'rmarkdown',
  'rpms', 'testthat'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'withr', 'covr', 'rprojroot',
  '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: 'data.table', 'laeken'

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

Packages suggested but not available for checking:
  'hexbin', 'RSQLite', 'quantreg', 'CompQuadForm', 'DBI', 'AER'

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

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', 'flexsurv', 'dplyr', 'ggplot2', 'rms', 'xlsx', 'rstan',
  'tibble', 'BH', 'RcppEigen', 'StanHeaders'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'readr', 'tidyverse', 'glmnet', 'factoextra', 'igraph',
  'useful'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survC1'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'np', 'doParallel', 'doRNG', 'foreach', 'TPmsm', 'Rcpp', 'ggplot2',
  'gridExtra', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'readr', 'rjags', 'R2jags', 'tidyverse', 'icenReg',
  'ICBayes', 'dplyr', 'rlang'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'dplyr', 'forcats', 'magrittr', 'purrr', 'stringr',
  'tibble', 'tidyr', 'gridExtra', 'ggplot2', 'scales', 'survminer',
  'cowplot', 'tidytidbits'

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

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

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

Packages suggested but not available for checking:
  'distr6', 'keras', 'pseudo', 'reticulate', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'copula', 'splines2', 'matrixcalc'

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'Rcpp', 'glmnet', 'RcppEigen'

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking: 'forcats', 'glue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'survJamda'
Packages required but not available:
  'survivalROC', 'ecodist', 'survcomp', 'survJamda.data'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'caret', 'ggplot2', 'ggpubr', 'pec',
  'randomForestSRC'

VignetteBuilder 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', 'ggpubr', 'gridExtra', 'magrittr', 'maxstat', 'scales',
  'broom', 'dplyr', 'tidyr', 'survMisc', 'purrr', 'tibble', 'rlang',
  'ggtext'

Packages suggested but not available for checking:
  'knitr', 'flexsurv', 'cmprsk', 'markdown', '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: 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'KMsurv', 'ggplot2', 'data.table', 'zoo', 'gridExtra',
  'km.ci', 'xtable'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/plots.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:
  'broom', 'dplyr', 'forcats', 'ggplot2', 'lifecycle', 'magrittr',
  'mvtnorm', 'purrr', 'rlang', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'survminer', '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: 'statmod', 'Rcpp', '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.
Package required but not available: 'numDeriv'

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
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: 'ggplot2', 'directlabels'

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

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

Packages suggested but not available for checking:
  'RColorBrewer', 'latticeExtra', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/survSNP.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', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'speedglm', 'SuperLearner', 'plyr', 'dplyr', 'tidyr', 'stringr',
  'ggplot2', 'ggsci'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'cmprsk', '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:
  'matrixStats', 'mixsqp', 'reshape', 'crayon', 'ggplot2'

Packages suggested but not available for checking:
  'curl', 'testthat', 'microbenchmark', 'knitr', 'rmarkdown',
  'L0Learn', 'genlasso', 'Rfast'

VignetteBuilder 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', 'fracdiff', 'robets', 'forecastHybrid'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vars', 'expm', 'reshape2', 'ggplot2', 'copula', 'clue', 'pbapply',
  'steadyICA', 'DEoptim', 'zoo', 'strucchange', 'Rcpp', 'RcppArmadillo'

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

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

Packages suggested but not available for checking:
  'covr', 'markdown', 'knitr', '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: 'svDialogs', 'svGUI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Undefined global functions or variables:
  levelplot wireframe
'LazyData' is specified without a 'data' directory
Packages required but not available: 'systemfonts', 'cpp11'

Packages suggested but not available for checking:
  'htmltools', 'testthat', 'xml2', 'covr', 'fontquiver', '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: 'htmlwidgets'

Packages suggested but not available for checking: 'htmltools', 'svglite'

Packages which this enhances but not available for checking:
  'gridSVG', 'knitr', 'XML', 'xml2'

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

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

VignetteBuilder packages required for checking but not installed:
  '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', 'knitr', 'markdown', 'testthat', '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: 'rjson', 'Rook', 'Rcpp'

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

Package suggested but not available for checking: 'svSocket'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvinecopulib', 'Rcpp', 'assertthat', 'univariateML', 'wdm',
  'fGarch', 'RcppEigen', 'RcppThread', 'BH'

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

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

Packages suggested but not available for checking: 'svHttp', 'svSocket'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rJava', 'covr', 'knitr', 'markdown', 'rmarkdown', 'testthat',
  '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:
  'reshape2', 'scales', 'gridExtra', 'dplyr', 'ggplot2', 'kernlab'

Packages suggested but not available for checking:
  'testthat', 'magrittr', 'xtable'

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: 'kernlab'

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: 'igraph', 'memoise', 'data.table'

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

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

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

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

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

Packages suggested but not available for checking:
  'svHttp', 'spelling', '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: 'gtools'

Package suggested but not available for checking: 'pvclust'

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'RUnit'
Package required but not available: 'svMisc'

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

Packages suggested but not available for checking:
  'doBy', 'NHANES', 'sampling'

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

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

Packages suggested but not available for checking:
  'pscl', 'knitr', 'markdown', '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:
  'jsonlite', 'plumber', '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: 'caret', 'Rdpack'

Packages suggested but not available for checking:
  'doParallel', 'e1071', 'foreach', 'ggplot2', 'glmnet', 'iterators',
  'kernlab', 'knitr', 'mlbench', 'ModelMetrics', 'plyr', 'pROC',
  'randomForest', 'recipes', 'remotes', 'reshape2', 'rmarkdown',
  '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: 'impute', 'amap', 'gplots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ROCR', 'reshape', '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:
  'e1071', 'LiblineaR', 'SparseM', 'kernlab', 'checkmate', 'BBmisc'

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', 'pack', 'stringr', 'xml2', 'colorspace'

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

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

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: 'spatstat.random'

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

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:
  'broom', 'dplyr', 'forecast', 'lubridate', 'tibble', 'tidyr',
  'timetk', 'rlang'

Packages suggested but not available for checking:
  'forcats', 'knitr', 'rmarkdown', 'testthat', 'purrr', 'readr',
  'robets', 'stringr', 'scales', 'tidyquant', 'tidyverse', 'fracdiff'

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

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

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

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: 'Rcpp'

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

VignetteBuilder 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', 'readr', 'rlang', 'stringr',
  'swfscDAS', 'swfscMisc', 'tidyr'

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:
  'dplyr', 'lubridate', 'magrittr', 'purrr', 'readr', 'rlang', 'sf',
  'swfscMisc', 'tidyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'kknn', 'mapdata', 'magrittr',
  'tibble', 'maps', 'rlang', 'sf', 'spatstat.geom', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'purrr', 'dplyr', 'stringr', 'rvest', 'pdftools', 'magrittr', 'xml2',
  'readr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'Hmisc', 'nleqslv', 'reshape2', 'plyr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'mvtnorm', 'spelling', 'Weighted.Desc.Stat', 'knitr',
  'rmarkdown', 'bookdown', '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:
  'swirl', 'stringr', 'yaml', 'rmarkdown', 'whisker', 'shiny',
  'shinyAce', 'base64enc', 'readr'

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

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

Package suggested but not available for checking: 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'IDPmisc'
Packages required but not available:
  'arm', 'lme4', 'maptools', 'blme', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'jsonlite', 'magrittr', 'purrr', 'stringr', 'tibble',
  'tidyr', 'crayon', 'httr', 'ggplot2'

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', 'expm', 'HiddenMarkov'

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

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:
  'dplyr', 'purrr', 'readr', 'Rcpp', 'tibble', 'tidyr', 'xts', 'zoo'

Packages suggested but not available for checking:
  'DEoptim', 'ggplot2', 'sf', '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:
  'SWMPr', 'EnvStats', 'RColorBrewer', 'broom', 'dplyr', 'flextable',
  'ggimage', 'ggplot2', 'ggthemes', 'lubridate', 'magrittr', 'officer',
  'purrr', 'rlang', 'scales', 'sf', 'tidyselect', 'tidyr'

Package suggested but not available for checking: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'zoo', 'data.table', 'httr', 'gridExtra', 'maptools',
  'oce', 'dplyr', 'openair', 'RColorBrewer', 'reshape2', 'tictoc',
  'tidyr', 'XML'

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

VignetteBuilder 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', 'zoo', 'dplyr', 'tidyr', 'readr', 'tibble', 'forcats',
  'stringr', 'rlang', 'rmarkdown', 'reshape2', 'ggplot2', 'ggmap',
  'magrittr', 'hydroTSM', 'jsonlite', 'sf', 'sp', 'lubridate',
  'segmented'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'glpkAPI', 'cplexAPI', 'clpAPI', 'lpSolveAPI'
Package unavailable to check Rd xrefs: 'glpkAPI'
Running examples in 'sybil-Ex.R' failed
The error most likely occurred in:

> ### Name: SYBIL_SETTINGS
> ### Title: Set and Get sybil Parameters
> ### Aliases: SYBIL_SETTINGS SOLVER METHOD TOLERANCE MAXIMUM ALGORITHM
> ###   OPT_DIRECTION USE_NAMES PATH_TO_MODEL SOLVER_CTRL_PARM
> ### Keywords: optimize
> 
> ### ** Examples
> 
>   ## show all current parameters
>   SYBIL_SETTINGS()
$MODELORG_VERSION
[1] "2.0"

$SOLVER
[1] "glpkAPI"

$METHOD
[1] "simplex"

$TOLERANCE
[1] 1e-06

$MAXIMUM
[1] 1000

$ALGORITHM
[1] "fba"

$OPT_DIRECTION
[1] "max"

$USE_NAMES
[1] FALSE

$PATH_TO_MODEL
[1] "."

$SOLVER_CTRL_PARM
  NA
1 NA

>   
>   ## show current setting for "SOLVER"
>   SYBIL_SETTINGS("SOLVER")
[1] "glpkAPI"
> 
>   ## change current solver to glpkAPI
>   SYBIL_SETTINGS("SOLVER", "glpkAPI")
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'glpkAPI'
Error in checkDefaultMethod(solver = value, method = "", probType = "",  : 
  package 'glpkAPI' not found
Calls: SYBIL_SETTINGS -> checkDefaultMethod
Execution halted
Error(s) in re-building vignettes:
--- re-building 'sybil.Rnw' using Sweave
Loading required package: Matrix
Loading required package: lattice
reading model description, ... OK
reading metabolite list ... OK
parsing reaction list ... OK
GPR mapping ... OK
sub systems ... OK
prepare modelorg object ... OK
validating object ... OK
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'glpkAPI'

Error: processing vignette 'sybil.Rnw' failed with diagnostics:
 chunk 13 
Error in checkDefaultMethod(solver, method, pType) : 
  package 'glpkAPI' not found

--- failed re-building 'sybil.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

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

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', 'sylly.de', 'sylly.en', 'sylly.es'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ./tests
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'clusterSim', 'XML', 'rgl', 'shapes', 'e1071', 'ade4', 'RSDA'

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

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

VignetteBuilder 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'

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

Packages suggested but not available for checking:
  'BGData', 'BEDMatrix', '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:
  'crayon', 'pracma', 'odeintr', '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', 'Rdpack', 'RcppArmadillo'

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

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

Packages suggested but not available for checking: 'ape', 'mpoly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'harmony', 'uwot', 'irlba', 'purrr', 'dplyr', 'ggplot2',
  'magrittr', 'data.table', 'tibble', 'tidyr', 'rlang', 'RColorBrewer',
  'ggrastr', 'ggrepel', 'RANN', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', '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:
  'OpenMx', 'metaSEM', 'Ryacas', '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: 'bigmemory.sri', 'Rcpp', 'uuid', 'BH'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: '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:
  'vegan', 'FD', 'permute', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'L1pack', 'Rdpack'

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

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

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

VignetteBuilder 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', 'lubridate', 'magrittr', 'sf', 'rnaturalearth',
  'rnaturalearthdata', 'metR', 'raster', 'RNCEP', 'stringr', 'tidyr',
  'tibble', 'kohonen'

Packages suggested but not available for checking:
  'maptools', 'ncdf4', 'rgeos', 'udunits2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'glue', 'covr', 'testthat', 'spelling'
'LazyData' is specified without a 'data' directory
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'parmigene', 'GenKern', 'igraph'

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

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

VignetteBuilder 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:
  'covr', 'haven', 'testthat'

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

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

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

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

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

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:
  'zoo', 'knitr', 'WASP', 'NPRED', 'rmarkdown', 'testthat', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'synthesis-Ex.R' failed
The error most likely occurred in:

> ### Name: data.gen.ar1
> ### Title: Generate predictor and response data from AR1 model.
> ### Aliases: data.gen.ar1
> 
> ### ** Examples
> 
> # AR1 model from paper with 9 dummy variables
> data.ar1<-data.gen.ar1(500)
> plot.ts(cbind(data.ar1$x,data.ar1$dp))
> 
> # Predictor Identifier
> NPRED::stepwise.PIC(data.ar1$x, data.ar1$dp)
Error in loadNamespace(x) : there is no package called 'NPRED'
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: 'stringdist'

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', 'magrittr', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'RColorBrewer', 'actuar', 'poisson',
  'ChainLadder'

VignetteBuilder 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', 'party', 'plyr', 'proto', 'polspline', 'randomForest',
  'ranger', 'classInt', 'mipfp', 'stringr'

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

Packages suggested but not available for checking: 'rgenoud', 'LowRankQP'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'curl', 'jsonlite'
Packages required but not available:
  'signal', 'tframe', 'ggplot2', 'reshape2', 'polynom', 'bitops', 'zoo'

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:
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'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: 'car', 'lmtest', 'sandwich'

Packages suggested but not available for checking: 'plm', 'sem'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'maotai', 'mclustcomp', 'rstiefel', 'scatterplot3d', 'RcppArmadillo'

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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  'tibble', 'tidyr'

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.
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: 'openxlsx'

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

Packages suggested but not available for checking:
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  'tidyr', 'tibble', 'gt'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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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: 'shiny', 'htmltools', 'knitr'

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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  'lubridate', 'purrr', 'R6', 'RCurl', 'rlist', 'stringr', 'urltools'

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: 'ggplot2', 'tables'

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

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Packages suggested but not available for checking:
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  'shinyFiles', 'fs', 'haven', 'yaml', 'sortable', 'latexpdf', 'csv',
  'xtable', 'shinyAce', 'R.utils'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'tibble', 'coro', 'vctrs'

Packages suggested but not available for checking:
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  'knitr', 'rmarkdown', 'vip', 'tidyverse', 'ggplot2', 'dplyr',
  'tidyr', 'purrr', 'tune', 'workflows'

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

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'
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  'rlang', 'tibble', 'tidyr', 'vctrs', 'cli', 'tidyselect', 'stringi',
  'pillar', 'kableExtra', 'DescTools'

Packages suggested but not available for checking:
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  'testthat'

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

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

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

> ### Name: aHDL
> ### Title: Alcohol and HDL Cholesterol: An Observational Study with 3
> ###   Control Groups
> ### Aliases: aHDL
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(aHDL)
> table(aHDL$grp,aHDL$grpL) # Short labels for plotting
           
              D   N   R   B
  Daily     406   0   0   0
  Never       0 406   0   0
  PastBinge   0   0   0 406
  Rarely      0   0 406   0
> boxplot(aHDL$age~aHDL$grp,xlab="Group",ylab="Age")
> boxplot(aHDL$education~aHDL$grp,xlab="Group",ylab="Education")
> table(aHDL$female,aHDL$grpL)
   
      D   N   R   B
  0 269 269 269 269
  1 137 137 137 137
> table(aHDL$z,aHDL$grpL)
   
      D   N   R   B
  0   0 406 406 406
  1 406   0   0   0
> 
> # The sets were also matched for is.na(aHDL$mmercury), for use
> # in Rosenbaum (2022a).  About half of the matched sets
> # have values for mmercury.
> table(is.na(aHDL$mmercury),aHDL$grp)
       
        Daily Never PastBinge Rarely
  FALSE   200   200       200    200
  TRUE    206   206       206    206
> 
> # Sensitivity analysis in Rosenbaum (2022b); see
> # also Rosenbaum (2014)
> y<-t(matrix(aHDL$hdl,4,406))
> y<-y[,c(1,3,2,4)]
> colnames(y)<-c("D","N","R","B")
> sensitivitymw::senmw(y,gamma=6,method="f")$pval
Error in loadNamespace(x) : there is no package called 'sensitivitymw'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'shiny'

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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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  'data.table', 'broom', 'colorRamps', 'minpack.lm', 'baseline'

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

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  'psych', 'sfsmisc', 'sirt', 'WrightMap'

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

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

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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manual.
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  'digest', 'htmltools'

Packages suggested but not available for checking:
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  'Matching', 'epitools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'vctrs', 'withr'

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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  'knitr', 'R6', 'rlang', 'tibble', 'tidyselect', 'vctrs', 'withr',
  'yaml'

Packages suggested but not available for checking:
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  'future', 'future.callr', 'googleCloudStorageR', 'gt', 'keras',
  'markdown', 'rmarkdown', 'paws', 'pingr', 'pkgload', 'processx',
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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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  'data.table', 'stringr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'DBI', 'arkdb', 'tibble', 'readr', 'rappdirs', 'rlang',
  'magrittr', 'stringi', 'progress', 'dbplyr', 'curl', 'jsonlite',
  'duckdb', 'contentid', 'R.utils'

Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'progress', 'utf8', 'crayon'

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

Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'GA', '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
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  'dbplyr', 'magrittr', 'hoardr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'xml2', 'jsonlite', 'foreach', 'ape', 'zoo', 'data.table',
  'tibble', 'bold', 'rredlist', 'rotl', 'ritis', 'worrms', 'natserv',
  'wikitaxa', 'R6', 'crayon', 'cli', 'phangorn', 'conditionz'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'taxa', 'taxize', 'stringdist', 'vegdata'

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

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

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

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:
  'RSQLite', 'R.utils', 'data.table', 'curl'

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: 'pbapply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'taxize', 'wikitaxa', 'plyr', 'sqldf', 'stringr', 'stringdist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'ggplot2', 'glue', 'lifecycle', 'rlang', 'scales',
  'tibble', 'vctrs'

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

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'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'tayloRswift-Ex.R' failed
The error most likely occurred in:

> ### Name: scale_color_taylor
> ### Title: Color scale for Taylor Swift colors
> ### Aliases: scale_color_taylor
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages required but not available: 'Rcpp', 'sp'

Packages suggested but not available for checking:
  'GISTools', 'RColorBrewer', 'rgeos'

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: 'signal', 'fdrtool'

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

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

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

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

VignetteBuilder 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', 'ranger', 'zoo', 'RcppRoll'

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:
  'mlt', 'mboost', 'variables', 'basefun', 'sandwich', 'coneproj'

Packages suggested but not available for checking:
  'TH.data', 'tram', 'partykit', 'latticeExtra', 'knitr', 'colorspace',
  'gamlss.data', 'trtf'

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

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

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

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:
  'ape', 'Rdpack', 'TreeDist', 'TreeTools', 'BH', '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:
  'dplyr', 'lubridate', 'purrr', 'rlang', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'spelling', 'covr', 'ggalt', 'ggplot2', '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:
  'normalp', 'mcmc', 'R.utils', 'coda', 'Rsolnp', 'BMS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'config', 'data.table', 'futile.logger', 'gmodels', 'matrixcalc',
  'matrixStats', 'nloptr', 'pbapply', 'pracma', 'rsvd', 'quadprog'

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: 'maxLik', 'Rdpack'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'viridis',
  'future.apply', 'tictoc', 'censReg', 'truncreg', 'microbenchmark'

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: '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:
  'ggplot2', 'lme4', 'reshape2', 'GSA', 'multtest', 'cowplot',
  'gtools', 'stringr'

Packages suggested but not available for checking:
  'BiocManager', 'foreach', 'doParallel', 'dearseq', 'knitr',
  'GEOquery', 'rmarkdown'

VignetteBuilder 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', 'oro.dicom', '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', 'truncnorm', 'mvtnorm', 'gridExtra', 'reshape', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', '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:
  'eRm', 'psychotools', 'ltm', 'numDeriv', 'colorspace', 'psych'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'mclust', 'mvtnorm', 'sn'
Running examples in 'tclust-Ex.R' failed
The error most likely occurred in:

> ### Name: DiscrFact
> ### Title: Discriminant Factor Analysis for tclust Objects
> ### Aliases: DiscrFact print.DiscrFact
> ### Keywords: hplot cluster robust multivariate
> 
> ### ** Examples
> 
> sig <- diag (2)
> cen <- rep (1, 2)
> x <- rbind(mvtnorm::rmvnorm(360, cen * 0,   sig),
+ 	       mvtnorm::rmvnorm(540, cen * 5,   sig * 6 - 2),
+ 	       mvtnorm::rmvnorm(100, cen * 2.5, sig * 50)
+ )
Error in loadNamespace(x) : there is no package called 'mvtnorm'
Calls: rbind ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'ttclust.R'
Running the tests in 'tests/ttclust.R' failed.
Complete output:
  > ##  VT::03.09.2016 - this will render the output independent
  > ##  from the version of the package
  > suppressPackageStartupMessages(library(tclust))
  > 
  > require(tclust)
  > require(mvtnorm)
  Loading required package: mvtnorm
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'mvtnorm'
  > #--- EXAMPLE 1 ------------------------------------------
  > 
  > set.seed(123)
  > sig <- diag (2)
  > cen <- rep (1,2)
  > x <- rbind(mvtnorm::rmvnorm(360, cen * 0,   sig),
  +             mvtnorm::rmvnorm(540, cen * 5,   sig * 6 - 2),
  +             mvtnorm::rmvnorm(100, cen * 2.5, sig * 50)
  +            )
  Error in loadNamespace(x) : there is no package called 'mvtnorm'
  Calls: rbind ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Errors in running code in vignettes:
when running code in 'tclust.rnw'

> options(prompt = "R> ", continue = "+  ", width = 70, 
+     useFancyQuotes = FALSE)

> library(tclust)

> mmar <- c(5.1, 4.1, 4.1, 1.1)

> og <- grey(0)

> set.seed(100)

> data(geyser2)

> clus <- tkmeans(geyser2, k = 3, alpha = 0.03)

> plot(clus, col = c(og, 2:4), tol.lwd = 1, tol.lty = 2)

> data(M5data)

> cl <- M5data[, "cluster"]

> plot(M5data[, 1:2], col = cl + 1, pch = cl + 1, main = "The M5data data set")

> data(M5data)

> x <- M5data[, 1:2]

> set.seed(100)

> res.a <- tclust(x, k = 3, alpha = 0.1, restr.fact = 1, 
+     restr = "eigen", equal.weights = TRUE, warnings = 1)

> res.c <- tclust(x, k = 3, alpha = 0.1, restr.fact = 1, 
+     restr = "deter", equal.weights = TRUE, warnings = 1)
Warning in .tkmeans.warn(O, ret) :
  Less than 50% of the iterations (44%) converged - please increase iter.max.

> res.d <- tclust(x, k = 3, alpha = 0.1, restr.fact = 50, 
+     restr = "eigen", equal.weights = FALSE)

> op <- par(mfrow = c(2, 2), mar = c(2.1, 2.1, 3.6, 
+     1.1))

> col <- c(og, 4, 2, 3)

> pch <- c(1, 4, 2, 3)

> plot(res.a, col = col, pch = pch, tol.lty = 2, xlab = "", 
+     ylab = "", main.pre = "(a)", main = "/r")

> plot(res.c, col = col, pch = pch, tol.lty = 2, xlab = "", 
+     ylab = "", main.pre = "(c)", main = "/r")

> plot(res.d, col = col, pch = pch, tol.lty = 2, xlab = "", 
+     ylab = "", main.pre = "(d)", main = "/r")

> par(op)

> library(mvtnorm)

  When sourcing 'tclust.R':
Error: there is no package called 'mvtnorm'
Execution halted

  'tclust.rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'tclust.rnw' using Sweave
Warning in .tkmeans.warn(O, ret) :
  Less than 50% of the iterations (44%) converged - please increase iter.max.

Error: processing vignette 'tclust.rnw' failed with diagnostics:
 chunk 4 (label = chunk4) 
Error in library(mvtnorm) : there is no package called 'mvtnorm'

--- failed re-building 'tclust.rnw'

SUMMARY: processing the following file failed:
  'tclust.rnw'

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

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

VignetteBuilder 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', 'numDeriv', 'RColorBrewer', 'future.apply', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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:
  'data.table', 'DBI', 'RMariaDB', 'numDeriv', 'RColorBrewer', 'sqldf'

Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'prettydoc', 'rmarkdown', 'htmlTable',
  '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', 'data.table', 'jsonlite', 'websocket'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'Rdpack', 'TDAstats', 'T4cluster', 'energy', 'ggplot2',
  'maotai', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'fastcluster', 'igraph'
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for 'hist'
mapper1D: no visible global function definition for 'dist'
mapper1D: no visible global function definition for 'as.dist'
mapper1D: no visible global function definition for 'hclust'
mapper1D: no visible global function definition for 'cutree'
mapper2D: no visible global function definition for 'dist'
mapper2D: no visible global function definition for 'as.dist'
mapper2D: no visible global function definition for 'hclust'
mapper2D: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'FNN', 'Rcpp', 'igraph', 'scales', 'BH', 'RcppEigen'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SPOT', 'twiddler', 'testit', 'adabag'

Packages suggested but not available for checking:
  'cmaes', 'e1071', 'ROCR', 'randomForest', 'rCMA', 'rSFA'

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.
Package required but not available: 'RcppSimdJson'

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

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

Package suggested but not available for checking: 'latticeExtra'

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

Packages suggested but not available for checking:
  'tuneR', 'alluvial', 'covr', 'testthat', 'devtools', 'GA',
  'sonicscrewdriver'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'pacman', 'shinythemes', 'shinydashboard', 'dplyr', 'DT',
  'actuar', 'markdown', 'knitr', 'data.table', 'Rcpp', 'rprojroot',
  'devtools', 'scales', 'yaml', 'magrittr', 'ggplot2', 'RcppNumerical',
  'miniUI', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'radarchart', 'networkD3', 'diagram',
  'DiagrammeR', 'visNetwork', 'metricsgraphics', 'leaflet', 'shinyAce',
  'plotly', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tkrplot', 'rgl', 'tcltk2', 'png', 'ggplot2', 'logspline',
  'maptools', 'R2wd', 'manipulate'
Packages required but not available: 'dplyr', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'units', 'checkmate', 'crayon', 'dplyr', 'furrr', 'future', 'glue',
  'magrittr', 'purrr', 'rlang', 'stringr'

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

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

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

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

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

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

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: 'httr', 'jsonlite'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'coda', 'cowplot', 'dplyr', 'fields', 'itertools',
  'mvtnorm', 'raster', 'scoringRules', 'stringr', 'foreach', 'ggplot2',
  'gtable', 'reshape2', 'scales', 'sp', 'Rcpp', 'RcppArmadillo',
  '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: 'curl', 'httr', 'jsonlite', 'R6'

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', 'httr', 'jsonlite', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'fs', 'gstat', 'magrittr', 'purrr', 'raster',
  'Rcpp', 'rlang', 'sf', 'sp', 'stringr', 'sys', 'tidyr', 'tidyselect',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rgdal', 'rmarkdown', 'RTriangle', 'stars', 'terrainmeshr',
  'tidyverse', '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:
  'tcltk2', 'tm', 'wordcloud', 'RColorBrewer', 'arules', 'arulesViz',
  'ggplot2', 'gridExtra'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > # These tests are more extensive and only need to run on travis, not on CRAN.
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'broom', 'dplyr', 'rootSolve', 'minpack.lm', 'AICcmodavg', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'ciftiTools', 'excursions', 'fMRIscrub', 'ica',
  'matrixStats', 'pesel', 'SQUAREM'

Packages suggested but not available for checking:
  'RNifti', 'covr', 'doParallel', 'foreach', 'knitr', 'rmarkdown',
  'INLA', 'testthat'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package 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', 'expint', 'numDeriv', 'tidyr'

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

Packages suggested but not available 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', 'plyr', 'reshape2', 'magrittr', 'scales',
  'plotly'

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.
Package required but not available: 'stringr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'JADE', 'fICA', 'Rcpp', 'tensor', 'tsBSS', 'ICtest', 'ggplot2',
  'abind', 'RcppArmadillo'

Package suggested but not available for checking: 'stochvol'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tensr', 'rTensor', 'TRES', 'abind', 'combinat', 'pracma', 'mvtnorm',
  'Rcpp'

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

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

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

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

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

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 suggested but not available for checking:
  'abind', 'glmnet', 'testthat', 'knitr', 'rmarkdown'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > library("TensorTest2D")
  > test_check("TensorTest2D")
  Error in test_check("TensorTest2D") : 
    could not find function "test_check"
  Execution halted
Packages required but not available:
  'tensor', 'rTensor', 'expm', 'abind', 'pracma'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
Undefined global functions or variables:
  ID
Package required but not available: 'rainbow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ergm', 'tergm', 'statnet.common', 'network', 'networkDynamic',
  'Rcpp', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ergm', 'network', 'networkDynamic', 'robustbase', 'coda',
  'statnet.common', 'purrr'

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

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

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

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: 'shiny', 'viridisLite'

Packages suggested but not available for checking:
  'colourpicker', 'knitr', 'readxl', 'rmarkdown', 'shinyjs',
  'spelling', '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: 'quadprog', 'maps', 'dichromat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'httr', 'raster', 'rgdal', 'magick', 'png', 'sf',
  'units', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'covr', 'progressr', 'knitr', 'rmarkdown', 'progress',
  'jpeg', 'tiff', 'brio'

VignetteBuilder 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', 'ncdf4', 'sf', 'deldir', 'XML', 'igraph'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'hash', 'rgl', 'randomcoloR', 'R6', 'sets', 'cxhull', 'scales',
  'english', 'interp', 'Rvcg'

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

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

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

VignetteBuilder 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', 'deSolve', 'Rcpp'

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

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

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'scales', 'reshape2', 'forcats', 'knitr'

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

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

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

Packages suggested but not available for checking:
  'covr', 'crayon', 'knitr', 'labelled', 'lubridate', 'openxlsx',
  'rmarkdown'

VignetteBuilder 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', 'lpSolve', 'foreach', 'logitnorm', 'crayon', 'RcppArmadillo'

Packages suggested but not available for checking:
  'lpsymphony', 'Rsymphony', 'gurobi', 'Rglpk', 'mirt', 'progress',
  'shiny', 'shinythemes', 'shinyWidgets', 'shinyjs', 'DT', 'knitr',
  'rmarkdown', 'kableExtra', 'testthat', 'pkgdown', 'pkgload'

VignetteBuilder 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', 'corrplot', 'cutpointr', 'dplyr', 'ggplot2', 'Morpho',
  'multcompView', 'tidyr', 'tmvtnorm', 'truncnorm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'knitr', 'rmarkdown', '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
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking: 'testthat', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/tester_introduction.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/tester_introduction.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'minerva', 'Hmisc', 'Rcpp'

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

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running examples in 'TestFunctions-Ex.R' failed
The error most likely occurred in:

> ### Name: add_zoom
> ### Title: add_zoom: Zoom in on region of another function. Allows you to
> ###   easily change an existing function so that [0,1]^n refers to a
> ###   subregion of the original function
> ### Aliases: add_zoom
> 
> ### ** Examples
> 
> banana(c(.5,.85))
[1] 0.9692332
> add_zoom(banana, c(0,.5), c(1,1))(c(.5,.7))
[1] 0.9692332
> add_zoom(banana, c(.2,.5), c(.8,1))(matrix(c(.5,.7),ncol=2))
[1] 0.9692332
> ContourFunctions::cf(banana)
Error in loadNamespace(x) : there is no package called 'ContourFunctions'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'fda', 'ggplot2', 'rgl', 'dplyr', 'ggpubr', 'stringr', 'tidyr',
  'pracma', 'utf8', 'knitr', 'rmarkdown'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rstudioapi', 'covr'
Packages required but not available:
  'brio', 'callr', 'cli', 'crayon', 'desc', 'digest', 'ellipsis',
  'evaluate', 'jsonlite', 'lifecycle', 'magrittr', 'pkgload', 'praise',
  'processx', 'ps', 'R6', 'rlang', 'waldo', 'withr'

Packages suggested but not available for checking:
  'covr', 'curl', 'diffviewer', 'knitr', 'mockery', 'rmarkdown',
  'rstudioapi', 'shiny', 'usethis', 'vctrs', '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:
  'assertthat', 'devtools', 'fs', 'magrittr', 'pkgload', 'rprojroot',
  'stringi', 'testthat', 'usethis'

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

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', 'tidyr', 'FactoMineR', 'magrittr', 'tibble',
  'ggrepel', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'purrr', 'abind', 'ggplot2', 'readr', 'stringr', 'lubridate',
  'narray', 'imputeTS', 'scales', 'tictoc', 'modeest', 'moments',
  'greybox', 'philentropy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clisymbols', 'crayon', 'data.table', 'fastmatch', 'hunspell',
  'hutils', 'magrittr', 'rstudioapi', 'zoo'

Packages suggested but not available for checking:
  'devtools', 'readr', 'rlang', 'stringi', 'testthat', 'tinytex'

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

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

VignetteBuilder 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', 'ggplot2', 'Rcpp'

Packages suggested but not available for checking:
  'gridExtra', 'knitr', 'rmarkdown', 'dplyr', 'tidyr', 'testthat',
  'devtools', 'ismev'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'details', 'fs', 'htmltools', 'knitr', 'lifecycle',
  'magick', 'magrittr', 'rematch2', 'rstudioapi', 'svgPanZoom',
  'whisker', 'xml2'

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'pdftools', 'rmarkdown', 'shiny', '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: 'httr'

Packages suggested but not available for checking:
  'broom', 'coda', 'ggplot2', 'huxtable', 'knitr', 'rmarkdown',
  'sandwich', 'testthat', 'lmtest'

Packages which this enhances but not available for checking:
  'AER', 'alpaca', 'betareg', 'Bergm', 'bife', 'biglm', 'brglm',
  'brms', 'btergm', 'dynlm', 'eha', 'erer', 'ergm', 'feisr', 'fGarch',
  'fixest', 'forecast', 'gamlss', 'gamlss.inf', 'gee', 'glmmTMB',
  'gmm', 'gnm', 'h2o', 'latentnet', 'lfe', 'lme4', 'lqmm', 'metaSEM',
  'mfx', 'mhurdle', 'miceadds', 'mlogit', 'mnlogit', 'MuMIn', 'oglmx',
  'ordinal', 'pglm', 'plm', 'relevent', 'rms', 'robust', 'simex',
  'spatialreg', 'spdep', 'speedglm', 'truncreg', 'VGAM', 'Zelig'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'text2vec', 'doParallel', 'foreach', 'stringr', 'stringi',
  'dplyr', 'kit', 'fastmatch', 'mlpack', 'qgraph', 'igraph',
  'magrittr', 'rlang'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'aws.signature', 'dplyr', 'googleAuthR', 'googleLanguageR', 'httr',
  'mscstts', 'tuneR', 'magrittr', 'knitr'

Packages suggested but not available for checking:
  'aws.polly', 'covr', 'rmarkdown', 'testthat', '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:
  'Rcpp', 'R6', 'data.table', 'rsparse', 'stringi', 'mlapi', 'lgr',
  'digest'

Packages suggested but not available for checking:
  'magrittr', 'udpipe', 'glmnet', 'testthat', 'covr', 'knitr',
  'rmarkdown', 'proxy'

VignetteBuilder 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', '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: 'tau', 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'english', 'glue', 'lexicon', 'mgsub', 'qdapRegex',
  'stringi', 'textshape'

Package suggested but not available for checking: 'testthat'

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

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: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'plyr', 'ggplot2', 'magrittr', 'stringr', 'purrr',
  'stopwords', 'textdata', 'tidytext', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rlang', 'text2vec', 'tfse', 'tibble', 'tokenizers'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'tidytext', 'tm', 'wordcloud', 'dplyr', 'plyr', 'udpipe',
  'RColorBrewer', 'ggplot2', 'glmnet', 'pdftools', 'doParallel',
  'pracma', 'forcats'

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.
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: 'distrom', 'gamlr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gtools', 'magrittr', 'text2vec', 'stopwords', 'stringr', 'Rcpp',
  'RcppProgress', 'RSpectra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'spelling', 'digest', 'dplyr', 'igraph', 'knitr', 'lda', 'rmarkdown',
  'SnowballC', 'stringi', 'testthat', 'tibble', 'tidyr', 'tidytext',
  'topicmodels', 'wordcloud'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'syuzhet', 'dplyr', 'tidyr', 'tidytext', 'tibble', 'tm', 'slam',
  'ggplot2', 'ggwordcloud', 'RColorBrewer'

Packages suggested but not available for checking:
  'tkrplot', 'SnowballC', 'readxl', 'jsonlite', 'ggrepel', 'ggpubr',
  'igraph', 'ggraph', 'ape', 'topicmodels', 'ca', 'corrr',
  'data.table', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "points", "text",
             "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
Package required but not available: 'data.table'

Packages suggested but not available for checking:
  'knitr', 'udpipe', 'BTM', 'igraph', 'graph', 'Rgraphviz', 'qgraph',
  'glasso', 'ggplot2', 'ggraph', 'ggforce', 'concaveman', 'ggrepel',
  'ggalt', 'uwot'

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

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

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

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

VignetteBuilder 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', 'stringi', 'tidyr', 'ggplot2', 'ggrepel',
  'cowplot', 'rlang', 'purrr', 'magrittr', 'parsnip', 'recipes',
  'rsample', 'reticulate', 'tune', 'workflows', 'yardstick', 'future',
  'furrr', 'overlapping'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'rio', 'glmnet', 'randomForest',
  'covr', 'xml2', 'ranger'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'antiword', 'curl', 'data.table', 'pdftools', 'readxl', 'rvest',
  'striprtf', 'textshape', 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'lifecycle', 'dplyr', 'generics', 'magrittr', 'purrr',
  'Rcpp', 'rlang', 'SnowballC', 'tibble', 'tidyr', 'tokenizers',
  'vctrs', 'glue'

Packages suggested but not available for checking:
  'covr', 'janitor', 'knitr', 'modeldata', 'rmarkdown',
  'sentencepiece', 'spacyr', 'stopwords', 'stringi', 'testthat',
  'text2vec', 'textfeatures', 'tokenizers.bpe', 'udpipe', 'wordpiece'

VignetteBuilder 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', 'NLP', 'Rcpp'

Packages suggested but not available for checking:
  'corrplot', 'knitr', 'SnowballC', 'xtable', 'testthat', 'plyr',
  'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'digest', 'dplyr', 'NLP', 'Rcpp', 'RcppProgress',
  'stringr', 'tibble', 'tidyr', 'BH'

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: 'data.table', 'slam', '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: 'systemfonts', 'cpp11'

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.
Packages required but not available:
  'koRpus.lang.en', 'dplyr', 'hunspell', 'koRpus', 'lexicon',
  'quanteda', 'SnowballC', 'stringi', 'textclean', 'textshape'

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', 'data.table', 'RcppArmadillo', 'BH'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tinytest'
Packages required but not available:
  'reticulate', 'tensorflow', 'rstudioapi', 'keras', 'purrr'

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

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

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

Packages suggested but not available for checking:
  'rlang', 'tensorflow', '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:
  'reticulate', 'tensorflow', 'magrittr', 'rlang', 'tidyselect',
  'generics', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'keras', 'rsample', 'rmarkdown', 'Metrics',
  'dplyr', 'tfestimators'

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

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

Packages suggested but not available for checking:
  'cloudml', 'knitr', 'pixels', 'processx', 'testthat', 'yaml',
  '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:
  'forge', 'magrittr', 'progress', 'reticulate', 'rlang', 'tensorflow',
  'tfruns', 'tidyselect', 'purrr', 'tibble', 'tidyr'

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

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'tfestimators', 'keras', 'rmarkdown', 'callr',
  'recipes', 'tibble', 'abind', 'fs'

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

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

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: 'sn', 'mvtnorm'

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: 'tframe'

Package suggested but not available for checking: 'googleVis'

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

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

Packages suggested but not available for checking:
  'tfdatasets', '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: 'tframe', 'timeSeries'

Packages suggested but not available for checking:
  'tfplot', 'zoo', 'xts', 'tis', 'WriteXLS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'base64enc', 'yaml', 'config', 'magrittr', 'whisker',
  'tidyselect', 'rlang', 'rstudioapi', 'reticulate'

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

VignetteBuilder 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', 'dapr'

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: 'XML'

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

Package suggested but not available for checking: 'testthat'

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

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

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

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

Packages suggested but not available for checking:
  'R.rsp', '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', '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: 'plumber', 'callr', 'geojsonsf'

Packages suggested but not available for checking:
  'igraph', 'covr', 'curl', 'devtools', 'knitr', 'rmarkdown',
  'testthat', 'edgebundle', 'ggplot2', 'maps', 'sf', 'ggraph'

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'
'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: 'httr', 'jsonlite'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'gdata', 'plyr', 'trtf', 'tram', 'rms', 'coin', 'ATR',
  'multcomp', 'gridExtra', 'vcd', 'colorspace', 'knitr'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/blood_loss_report.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/blood_loss_report.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available:
  'askpass', 'httr', 'R6', 'raster', 'XML'

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

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

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

Packages suggested but not available for checking:
  'withr', 'sysfonts', 'showtext', 'Cairo', 'systemfonts', 'ragg',
  'knitr', 'rmarkdown', 'htmltools', 'shiny', 'bslib', 'testthat',
  'gganimate', 'vdiffr', 'svglite', 'jsonlite', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'dplyr', 'generics', 'purrr', 'RANN', 'rlang', 'ROSE',
  'tibble', 'unbalanced', 'withr'

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

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

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: 'tiff', 'png'

Package suggested but not available for checking: 'fields'

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

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

Package suggested but not available for checking: 'covr'

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

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:
  'assertthat', 'crayon', 'devtools', 'dplyr', 'ggplot2', 'lazyeval',
  'lubridate', 'magrittr', 'officer', 'purrr', 'readr', 'rvg',
  'stringi', 'stringr', 'tidyr'

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

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

Package which this enhances but not available for checking: 'testthat'
Package unavailable to check Rd xrefs: 'testthat'
Package required but not available: 'htmlwidgets'

Packages suggested but not available for checking: 'shiny', 'htmltools'

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

Packages suggested but not available for checking:
  'ids', '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', 'rlang', 'magrittr', 'httr', 'xml2'

Packages suggested but not available for checking: 'ncdf4', 'testthat'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mvtnorm'
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in 'threeboost-Ex.R' failed
The error most likely occurred in:

> ### Name: geeboost
> ### Title: GEEBoost
> ### Aliases: geeboost
> 
> ### ** Examples
> 
> # Generate some test data
> library(mvtnorm)
Error in library(mvtnorm) : there is no package called 'mvtnorm'
Execution halted
Packages required but not available:
  'dipsaus', 'xml2', 'shiny', 'digest', 'freesurferformats',
  'jsonlite', 'stringr', 'htmlwidgets', 'R6', 'gifti', 'oro.nifti'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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:
  'igraph', 'htmlwidgets', 'base64enc', 'crosstalk'

Package suggested but not available for checking: 'maps'

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:
  'dplyr', 'httr', 'readxl', 'readr', 'jsonlite', 'purrr', 'janitor',
  'tidyr', 'tidyselect', 'anytime', 'tibble', 'curl'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'scales',
  'stringi', 'ggrepel', 'fixerapi'

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

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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.
Package required but not available: 'Formula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ClassDiscovery', 'PCDimension', 'colorspace', 'movMF', 'ade4',
  'oompaBase'

Package suggested but not available for checking: 'NbClust'

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

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

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.
Packages required but not available:
  'Rcpp', 'climate', 'dplyr', 'aiRthermo'

Packages suggested but not available for checking:
  'RadioSonde', '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', 'dplyr', 'knitr', 'lavaan', 'magrittr', 'MplusAutomation',
  'mvtnorm', 'RcppParallel', 'rlang', 'rstan', 'rstantools', 'tibble',
  'tidyr', 'BH', 'RcppEigen', 'StanHeaders'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ellipsis', 'fansi', 'lifecycle', 'magrittr', 'pillar', 'pkgconfig',
  'rlang', 'vctrs'

Packages suggested but not available for checking:
  'bench', 'bit64', 'blob', 'brio', 'callr', 'cli', 'covr', 'crayon',
  'DiagrammeR', 'dplyr', 'evaluate', 'formattable', 'ggplot2', 'hms',
  'htmltools', 'knitr', 'lubridate', 'mockr', 'nycflights13',
  'pkgbuild', 'pkgload', 'purrr', 'rmarkdown', 'stringi', 'testthat',
  'tidyr', 'withr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'glue', 'hms', 'lubridate', 'purrr', 'Rcpp',
  'rlang', 'tibble', 'tidyselect', 'vctrs', 'zoo', 'lifecycle'

Packages suggested but not available for checking:
  'broom', 'covr', 'gapminder', '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:
  'crayon', 'rlang', 'vctrs', 'purrr', 'tibble'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.LoadTickDataHK: no visible global function definition for 'read.csv'
.LoadTickDataSHSZ: no visible global function definition for 'read.csv'
DrawDown: no visible global function definition for 'na.omit'
PerformanceReport: no visible global function definition for
  'aggregate'
PerformanceReport: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package required but not available: 'hash'

Packages suggested but not available for checking:
  'testthat', 'combiter', 'dplyr', 'tidyr', 'reshape2', 'ggplot2'

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'
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: 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').
'LazyData' is specified without a 'data' directory
Packages required but not available: 'chron', 'data.table', 'fields'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'chron', '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:
  'ggdist', 'dplyr', 'tidyr', 'ggplot2', 'coda', 'rlang',
  'arrayhelpers', 'tidyselect', 'tibble', 'magrittr', 'posterior',
  'withr', 'vctrs'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'purrr', 'forcats', 'vdiffr', 'svglite',
  'rstan', 'rstantools', 'runjags', 'rjags', 'jagsUI', 'rstanarm',
  'emmeans', 'broom', 'dotwhisker', 'MCMCglmm', 'bayesplot', 'modelr',
  'brms', 'cowplot', 'covr', 'gdtools', 'rmarkdown', 'ggrepel',
  'bindrcpp', 'RColorBrewer', 'gganimate', 'gifski', 'png', 'pkgdown',
  'distributional', 'transformr'

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

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

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:
  'magrittr', 'dplyr', 'stringr', 'tidyselect', 'purrr', 'janitor',
  'tibble', 'rlang', 'lubridate', 'scales', 'ggplot2', 'rlist', 'OneR',
  'strex', 'ClusterR', 'framecleaner', 'xgboost', 'badger'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'arulesCBA', 'embed', 'woeBinning', 'recipes'

VignetteBuilder 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', 'modelr', 'purrr', 'rlang', 'tidyr'

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

Packages suggested but not available for checking:
  'broom', 'ggplot2', 'ggforce', '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:
  'httr', 'sf', 'dplyr', 'tigris', 'stringr', 'jsonlite', 'purrr',
  'rvest', 'tidyr', 'rappdirs', 'readr', 'xml2', 'units', 'rlang',
  'crayon'

Packages suggested but not available for checking:
  'ggplot2', 'survey', 'srvyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'knitr', 'magick', 'rsvg', 'rlang', 'testthat',
  'htmlwidgets', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'palmerpenguins', 'tidyverse', 'dplyr', 'covr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cli', 'cmprsk', 'dplyr', 'ggplot2', 'gtsummary', 'hardhat',
  'purrr', 'rlang', 'stringr', 'tibble', 'tidyr'

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

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

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

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

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', '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:
  'badger', 'pacman', 'framecleaner', 'validata', 'presenter',
  'autostats', 'tidybins'

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

VignetteBuilder package required for checking but not installed: 'simplermarkdown'
Packages required but not available:
  'jsonlite', 'yaml', 'dplyr', 'magrittr', 'visNetwork', 'htmlwidgets',
  'webshot'

Packages suggested but not available for checking:
  '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: 'clipr', 'knitr', 'rstudioapi'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'assertthat', 'dplyr', 'ggplot2', 'magrittr', 'purrr', 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'dplyr', 'emoji', 'purrr', 'stringr', 'tibble', 'tidyr'

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

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: 'rmarkdown', 'knitr'

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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Packages suggested but not available for checking:
  'remotes', 'magrittr', 'tidyr', 'dplyr', 'testthat', 'covr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'nycflights13', 'pryr', 'tidyr', 'ggplot2',
  'dplyr', 'bench', 'testthat'

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

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

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  'rlang', 'tidyr', 'viridis', 'RColorBrewer', 'stringr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'stringr', 'magrittr', 'purrr', 'sf', 'rlang'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'tibble', 'dplyr', 'igraph', 'magrittr', 'rlang', 'R6', 'Rcpp',
  'tidyr', 'pillar'

Packages suggested but not available for checking:
  'network', 'data.tree', 'ape', 'graph', 'testthat', 'covr',
  'seriation', 'netrankr', 'influenceR', 'NetSwan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'tidyr', 'rlang', 'purrr', 'tibble',
  'ComplexHeatmap', 'viridis', 'circlize', 'RColorBrewer', 'lifecycle',
  'dendextend', 'patchwork'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'vdiffr', 'BiocManager', 'knitr',
  'rmarkdown', 'qpdf', 'covr', 'roxygen2', 'forcats', 'ggplot2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'cli', 'crayon', 'DBI', 'dbplyr', 'dplyr', 'httr', 'lubridate',
  'rappdirs', 'readr', '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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  'assertthat', 'jsonlite', 'purrr', 'dplyr', 'magrittr', 'tidyr',
  'tibble', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'ggplot2', 'rmarkdown', 'forcats', 'wordcloud',
  'viridis', 'listviewer', 'igraph', 'RColorBrewer', 'covr', 'vctrs',
  'lubridate', 'rprojroot'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'rstudioapi', 'tibble', 'usethat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'generics', 'gtools', 'mvrsquared', 'Rcpp', 'rlang',
  'stringr', 'tibble', 'tidyr', 'tidytext', 'RcppArmadillo',
  'RcppProgress', 'RcppThread'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'dplyr', 'ggplot2', 'gtable', 'mclust', 'mix', 'MplusAutomation',
  'tibble'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cli', 'conflicted', 'dials', 'dplyr', 'ggplot2', 'hardhat',
  'infer', 'modeldata', 'parsnip', 'purrr', 'recipes', 'rlang',
  'rsample', 'rstudioapi', 'tibble', 'tidyr', 'tune', 'workflows',
  'workflowsets', 'yardstick'

Packages suggested but not available for checking:
  'covr', 'glue', 'knitr', 'rmarkdown', 'testthat', 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'assertthat', 'dplyr', 'jsonlite', 'magrittr', 'purrr', 'rlang',
  'stringr', 'tibble'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'dplyr', 'ggplot2', 'magrittr', 'rlang', 'tibble', '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:
  'dplyr', 'forcats', 'magrittr', 'ncdf4', 'ncmeta', 'purrr',
  'RNetCDF', 'rlang', 'tibble', 'tidyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'dplyr', 'forcats', 'janitor', 'lubridate', 'magrittr', 'purrr',
  'rlang', 'stringr', 'tibble', 'tidyr', 'vroom', 'tidyselect'

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:
  'rlang', 'tidyselect', 'dplyr', 'vctrs', 'tibble', 'scales',
  'ggplot2', 'styler', 'purrr', 'ggstance', 'stringr', 'withr',
  'tidyr', 'digest', 'rioja'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'vegan', 'patchwork', 'forcats',
  '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:
  'xml2', 'tokenizers', 'stringr', 'tibble', 'dplyr', 'readr'

Packages suggested but not available for checking:
  'europepmc', 'tidytext', 'rmarkdown', '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:
  'rsample', 'tidyr', 'dplyr', 'rstanarm', 'rlang', 'purrr', 'tibble',
  'generics', 'ggplot2', 'vctrs', 'tune', 'workflowsets'

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

VignetteBuilder 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', 'purrr', 'knitr', 'generics', 'stringr', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'testthat', 'randomForest', 'ranger', 'earth', 'rmarkdown',
  'nycflights13', 'RSQLite', 'DBI', 'covr', 'xgboost', 'Cubist',
  'mlbench', 'partykit', 'yaml', 'parsnip', 'modeldata'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lubridate', 'PerformanceAnalytics', 'quantmod', 'dplyr', 'ggplot2',
  'jsonlite', 'httr', 'curl', 'lazyeval', 'magrittr', 'purrr',
  'Quandl', 'riingo', 'readr', 'alphavantager', 'stringr', 'tibble',
  'tidyr', 'timetk', 'timeDate', 'TTR', 'xts', 'rlang', 'tidyselect',
  'rstudioapi', 'crayon', 'cli', 'janitor'

Packages suggested but not available for checking:
  'tidyverse', 'tibbletime', 'forcats', 'broom', 'knitr', 'rmarkdown',
  'testthat', 'scales', 'Rblpapi', '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:
  'dplyr', 'lubridate', 'queryparser', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'covr', 'DBI', 'dbplyr', 'dtplyr', 'nycflights13', 'RSQLite',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'future', 'dplyr', 'httr', 'jsonlite', 'magrittr', 'xml2', 'stringr',
  'purrr', 'tidyr', 'labelled', 'furrr'

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:
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  'tidyr', '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.
Packages required but not available:
  'dplyr', 'ellipsis', 'glue', 'lifecycle', 'magrittr', 'purrr',
  'rlang', 'tibble', 'tidyselect', 'vctrs', 'cpp11'

Packages suggested but not available for checking:
  'covr', 'data.table', 'jsonlite', 'knitr', 'readr', 'repurrrsive',
  'rmarkdown', 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  'anytime', 'rlang', 'glue', 'vctrs', 'tidyselect'

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

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

Packages suggested but not available for checking:
  'AmesHousing', 'dplyr', 'C50', 'Cubist', 'rpart.plot', 'modeldata',
  'testthat', 'mlbench', 'knitr', 'rmarkdown', 'pander'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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Packages suggested but not available for checking:
  'covr', 'crayon', 'dplyr', 'knitr', 'magrittr', 'rmarkdown',
  '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:
  'OpenMx', 'ggplot2', 'lavaan', 'MplusAutomation', 'igraph', 'psych',
  'gtable'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr', 'stringr', 'covr',
  'tidyLPA', 'poLCA', 'umx'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ttservice', 'SeuratObject', 'Seurat', 'tibble', 'dplyr', 'magrittr',
  'tidyr', 'ggplot2', 'rlang', 'purrr', 'lifecycle', 'plotly',
  'tidyselect', 'ellipsis', 'pillar', 'stringr', 'cli', 'fansi'

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', 'ellipsis', 'glue', 'purrr', 'rlang', 'smd', 'tidyr',
  'tidyselect'

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:
  'checkmate', 'cli', 'crayon', 'dplyr', 'pillar', 'Rcpp', 'tibble',
  'vctrs', 'testthat'

Packages suggested but not available for checking:
  'ape', 'bioseq', 'Biostrings', 'covr', 'knitr', 'lifecycle', 'purrr',
  'seqinr', 'spelling', 'rmarkdown', 'testthat', 'withr', 'rlang',
  'mockr'

VignetteBuilder 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', 'purrr', 'stringr', 'readr', 'jsonlite', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
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Packages suggested but not available for checking:
  'dplyr', '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:
  'magrittr', 'tibble', 'dplyr', 'ggplot2', 'tidyr', 'forcats',
  'rlang', 'kernlab', 'LowRankQP', 'rgenoud', 'optimx'

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', 'glue', 'lifecycle', 'magrittr', 'pillar', 'rlang',
  'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'bit64', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'generics', 'hunspell', 'janeaustenr', 'lifecycle', 'purrr',
  'rlang', 'stringr', 'tibble', 'tokenizers', 'vctrs'

Packages suggested but not available for checking:
  'broom', 'covr', 'data.table', 'ggplot2', 'knitr', 'mallet', 'NLP',
  'quanteda', 'readr', 'reshape2', 'rmarkdown', 'scales', 'stm',
  'stopwords', 'testthat', 'textdata', 'tidyr', 'tm', 'topicmodels',
  'vdiffr', 'wordcloud', '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:
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  'tidyselect', 'extrafont', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gtfsio', 'dplyr', 'data.table', 'httr', 'rlang', 'sf', 'hms',
  'digest', 'checkmate', 'geodist'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown', 'rmarkdown', 'ggplot2', 'scales',
  '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:
  'tidybayes', 'purrr', 'tidyr', 'dplyr', 'readr', 'rlang'

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

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

VignetteBuilder 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', 'dplyr', 'lazyeval', 'magrittr', 'rlang', 'tibble', 'tidyr',
  'tidyselect', 'yulab.utils', 'pillar'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc', '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:
  'readxl', 'rvest', 'lubridate', 'purrr', 'readr', 'rstudioapi',
  'xml2', 'httr', 'jsonlite', 'magrittr', 'usethis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'dplyr', 'fuzzyjoin', 'ggplot2', 'httr', 'jsonlite',
  'magrittr', 'purrr', 'sf', 'tigris'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cli', 'crayon', 'dbplyr', 'dplyr', 'dtplyr', 'forcats',
  'googledrive', 'googlesheets4', 'ggplot2', 'haven', 'hms', 'httr',
  'jsonlite', 'lubridate', 'magrittr', 'modelr', 'pillar', 'purrr',
  'readr', 'readxl', 'reprex', 'rlang', 'rstudioapi', 'rvest',
  'stringr', 'tibble', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'covr', 'feather', 'glue', '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', 'magrittr', 'quantreg', 'rlang', 'classInt', 'ggplot2',
  'fastDummies'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'shiny', 'remotes', 'vpc', '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', 'dplyr', 'tidyr', 'WikidataR', 'stringr', 'glue', 'DBI',
  'RSQLite', 'tibble', 'purrr', 'usethis', 'WikidataQueryServiceR',
  'fs', 'rlang', 'progress', 'jsonlite', 'pool', 'WikipediR'

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

VignetteBuilder 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', 'piton'

Packages suggested but not available for checking:
  'testthat', 'here', 'knitr', 'rmarkdown', 'readxl', 'dplyr', 'tidyr',
  'purrr', 'tibble', 'ggplot2', 'cellranger', 'openxlsx', 'rlang'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'hexbin', 'qualV', 'klaR', 'som'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'alakazam', 'shazam', 'dplyr', 'doParallel', 'foreach',
  'gridExtra', 'gtools', 'iterators', 'lazyeval', 'rlang', 'stringi',
  'tidyr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'magrittr', 'rgdal', 'sp', 'rappdirs', 'maptools', 'httr',
  'uuid', 'sf', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggthemes', 'leaflet', 'knitr', 'rgeos',
  'tidycensus'

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

Packages suggested but not available for checking:
  'evaluate', 'formatR', 'ggplot2', 'knitr', 'maps', 'scales',
  'stringr', 'testthat', 'withr'

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

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

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

Packages suggested but not available for checking:
  'tinytest', 'simplermarkdown', 'curl', 'bit64', 'palmerpenguins',
  'nycflights13', 'data.table', 'tibble'

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

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

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'knitr', 'rmarkdown', '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:
  'APfun', 'raster', 'rgeos', 'sp', '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:
  'clue', 'ggplot2', 'igraph', 'lwgeom', 'sf', 'smoothr'

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

VignetteBuilder 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', 'rgdal', 'raster', 'png'

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

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

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

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

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

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

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

Package suggested but not available for checking: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'dplyr', 'lubridate', 'stringr', 'futile.logger', 'ggplot2',
  'gtable', 'mtconnectR'

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

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

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

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

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', '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: 'lubridate', 'timeDate'

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

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

Package suggested but not available for checking: 'mets'

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

Package suggested but not available for checking: 'timereg'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
Packages required but not available: 'gss', 'pheatmap', 'reshape'

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:
  'RPostgres', 'jsonlite', 'data.table', 'xts', 'DBI'

Packages suggested but not available for checking:
  'openxlsx', 'rstudioapi', 'dygraphs', '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:
  'forecast', 'locfit', 'jsonlite', 'trend', 'tseries'

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

Packages suggested but not available for checking:
  'RUnit', 'robustbase', 'xts', 'PerformanceAnalytics', 'fTrading'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'rsample', 'dplyr', 'ggplot2', 'forcats', 'stringr',
  'plotly', 'lubridate', 'padr', 'purrr', 'readr', 'stringi', 'tibble',
  'tidyr', 'xts', 'zoo', 'rlang', 'tidyselect', 'slider', 'anytime',
  'timeDate', 'forecast', 'tsfeatures', 'hms', 'assertthat', 'generics'

Packages suggested but not available for checking:
  'tidyquant', 'tidymodels', 'modeltime', 'workflows', 'parsnip',
  'tune', 'yardstick', 'tidyverse', 'knitr', 'rmarkdown', 'robets',
  'broom', 'scales', 'testthat', 'fracdiff', 'timeSeries', 'tseries',
  'roxygen2', '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: 'XML', 'phangorn'

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

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

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

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

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:
  'fields', 'deSolve', 'nnls', 'colorspace', 'minpack.lm', 'gclus',
  'gplots'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Runuran'
Package unavailable to check Rd xrefs: 'Runuran'
Packages suggested but not available for checking: 'testthat', 'rstudioapi'
Running 'testthat.R'
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: 'chk'

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', 'knitr', 'rmarkdown'

Package suggested but not available for checking: '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:
  'BiocManager', 'clusterProfiler', 'dplyr', 'limma', 'org.Hs.eg.db',
  'stringr', 'tibble', 'pheatmap', 'ggplot2', 'survminer', 'patchwork'

Packages suggested but not available for checking:
  'testthat', 'AnnoProbe', 'GEOquery', 'Biobase', 'VennDiagram',
  'FactoMineR', 'factoextra', 'knitr', 'rmarkdown', 'cowplot',
  'ggpubr', 'ggplotify', 'tidyr', 'labeling', 'Rtsne', 'scatterplot3d',
  'ComplexHeatmap', 'circlize'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'tinylabels-Ex.R' failed
The error most likely occurred in:

> ### Name: label_variable
> ### Title: Label Variables Using Pipes
> ### Aliases: label_variable label_variables
> 
> ### ** Examples
> 
>   library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'brew', 'R.utils'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'dplyr', 'ggplot2', 'gt', 'jsonlite', 'magrittr', 'purrr',
  'rlang', 'rvest', 'stringr', 'xml2', 'R.utils'

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

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

Packages suggested but not available for checking: 'testit', 'rstudioapi'

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

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: 'mclust', 'TeachingDemos', 'DescTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'dplyr', 'magrittr', 'stringi', 'cpp11'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'loo',
  'ggplot2', 'gridExtra', 'maptools', 'rgeos', 'sp', 'spdep', 'broom',
  'spam', 'ggpubr', 'callr', 'Rdpack', 'BH', 'RcppEigen', 'StanHeaders'

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: 'gtools', 'inline', 'Rcpp', 'stringr'

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

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: 'reshape', 'scales'

Packages which this enhances but not available for checking:
  'zoo', 'ggplot2'
Package unavailable to check Rd xrefs: 'ggplot2'
Packages required but not available:
  'dplyr', 'ggplot2', 'glue', 'cowplot', 'ggridges', 'purrr', 'tibble',
  'snow'

Packages suggested but not available 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: 'dplyr'
Package required but not available: 'Iso'

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

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'R.utils'

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

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'mvtnorm', 'flexmix'
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
Packages unavailable to check Rd xrefs: 'flexmix', 'modeltools'
Package required but not available: 'mvtnorm'

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

Packages suggested but not available for checking:
  'evd', 'knitr', 'magrittr', 'lmom', 'Lmoments', 'rmarkdown'

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

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

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/tlm.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/tlm.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'Rcpp', 'RcppEigen', 'BH'

Package suggested but not available for checking: 'mvtnorm'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tmaptools', 'sf', 'stars', 'units', 'RColorBrewer', 'viridisLite',
  'classInt', 'htmltools', 'htmlwidgets', 'widgetframe', 'leaflet',
  'leafsync', 'leafem', 'abind', 'rlang'

Packages suggested but not available for checking:
  'rmapshaper', 'rmarkdown', 'knitr', 'png', 'cartogram', 'osmdata',
  'ggplot2', 'dplyr', 'tidyr', 'shiny', 'testthat', 'covr', 'av',
  'gifski', 's2'

VignetteBuilder 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', 'lwgeom', 'stars', 'units', 'magrittr', 'RColorBrewer',
  'viridisLite', 'dichromat', 'XML'

Packages suggested but not available for checking:
  'tmap', 'rmapshaper', 'osmdata', 'OpenStreetMap', 'raster', 'png',
  'shiny', 'shinyjs'

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

Package suggested but not available for checking: 'numDeriv'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tm'
Note: found 134043 marked UTF-8 strings
Packages required but not available: 'httr', 'jsonlite', 'stringi'

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

Packages suggested but not available for checking: 'ggplot2', 'reshape2'

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

Packages suggested but not available for checking:
  'SuperLearner', 'e1071', 'randomForest', 'polspline', 'gam', 'knitr'

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

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

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

Packages suggested but not available for checking: 'dbarts', 'gam', 'ROCR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'beeswarm', 'tagcloud', 'XML', 'plotwidgets', 'RColorBrewer',
  'gplots', 'colorDF'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'pca3d', 'R.rsp', 'dplyr'

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

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

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: 'NLP', 'tm'

Package suggested but not available for checking: 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DSL', 'tm', 'NLP', 'slam'

Package suggested but not available for checking: 'XML'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'koRpus', 'sylly', 'tm', 'NLP'

Packages suggested but not available for checking:
  'koRpus.lang.en', '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: 'NLP', 'tm', 'xml2', 'ISOcodes'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'NLP', 'tm', 'boilerpipeR', 'RCurl', 'XML', 'RJSONIO'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'reshape2'

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

Packages suggested but not available for checking:
  'antiword', 'filehash', 'pdftools', 'Rcampdf', 'Rgraphviz',
  'Rpoppler', 'SnowballC', 'testthat', 'tm.lexicon.GeneralInquirer'

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: 'dplyr'

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

Packages suggested but not available for checking:
  'roxygen2', 'eRm', 'knitr', 'prettydoc', 'psychotools', 'testthat',
  'rmarkdown', 'dexterMST'

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: 'mvtnorm', 'gmm'

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', 'tmvmixnorm'

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

> ### Name: tbc
> ### Title: Temporal betweenness centrality
> ### Aliases: tbc
> 
> ### ** Examples
> 
> # Create a list of adjacency matrices, plot the corresponding graphs
> # (using the igraph package) and calculate tbc
> 
> A1 <- matrix(c(0,1,0,0,0,0,
+                1,0,1,0,0,0,
+                0,1,0,0,0,0,
+                0,0,0,0,0,0,
+                0,0,0,0,0,0,
+                0,0,0,0,0,0), ncol=6)
> 
> A2 <- matrix(c(0,0,0,0,0,0,
+                0,0,1,0,0,0,
+                0,1,0,1,1,0,
+                0,0,1,0,0,0,
+                0,0,1,0,0,0,
+                0,0,0,0,0,0), ncol=6)
> 
> A3 <- matrix(c(0,0,0,0,0,0,
+                0,0,0,0,0,0,
+                0,0,0,0,0,0,
+                0,0,0,0,0,0,
+                0,0,0,0,0,0,
+                0,0,0,0,0,0), ncol=6)
> 
> A4 <- matrix(c(0,1,0,0,0,0,
+                1,0,0,1,0,0,
+                0,0,0,0,0,0,
+                0,1,0,0,0,0,
+                0,0,0,0,0,0,
+                0,0,0,0,0,0), ncol=6)
> 
> library(igraph)
Error in library(igraph) : there is no package called 'igraph'
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: 'igraph'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'vcr', '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:
  'htmlwidgets', 'htmltools', 'magrittr', 'rlang', 'shiny',
  'shinyWidgets'

Packages suggested but not available for checking:
  'apexcharter', 'knitr', 'rmarkdown', 'scales', '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:
  'numDeriv', 'tibble', 'Rdpack', 'Formula', 'prediction', 'margins',
  'generics'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'AER', 'censReg', 'dplyr',
  'ggplot2', 'modelsummary', 'bookdown', 'cmtest'

VignetteBuilder 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', 'bit', 'rgdal'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'getPass', 'glue', 'httr', 'jsonlite',
  'keyring', 'lubridate', 'magrittr', 'prettyunits', 'purrr',
  'rstudioapi', 'parsedate'

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.
Packages required but not available: 'igraph', 'nloptr', 'Rmpfr', 'EQL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', '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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringi', 'Rcpp', 'SnowballC'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'stopwords', '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: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'PROJ', 'sf', 'tibble', 'rlang', 'purrr',
  'stringr', 'readr', 'lifecycle'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'RColorBrewer', 'ggplot2', 'geojsonsf',
  'cancensus', 'tidycensus', 'spelling', 'readxl', '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: 'plyr', 'dplyr', 'reshape2', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BiasedUrn', 'dplyr', 'glmnet', 'latticeExtra', 'lhs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'calibrate', 'HardyWeinberg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'data.table', 'Rdpack', 'nortest'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'knitr', 'rmarkdown', 'pander', 'XML', 'httr',
  'RCurl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'imager', 'ggplot2', 'cowplot', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crayon', 'testthat'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixStats', 'ggplot2', 'reshape2', 'tibble'

Package suggested but not available for checking: 'diffobj'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'slam', 'topicmodels'

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: 'torch'

Packages suggested but not available for checking:
  'udpipe', 'word2vec', 'uwot', 'tinytest', 'textplot', 'ggrepel',
  'ggalt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'modeltools', 'slam', 'tm'

Packages suggested but not available for checking:
  'lasso2', 'lda', 'OAIHarvester', 'SnowballC', 'corpus.JSS.papers'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RSpectra', 'combinat', 'quadprog', 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'gplots'

Packages suggested but not available for checking:
  'knitr', 'RGtk2', 'gWidgets2', 'gWidgets2RGtk2'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/TopKLists.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'gdistance', 'plotly', 'raster', 'RColorBrewer', 'scales',
  '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: 'graph', 'gRbase', 'qpgraph', 'fields'

Package suggested but not available for checking: 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'markdown'
Packages required but not available:
  'ggplot2', 'dplyr', 'stringr', 'readr', 'scales', 'ggrepel', 'egg',
  'gridExtra', 'magrittr', 'toprdata'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'markdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'torch', 'fs', 'rlang', 'rappdirs', 'glue', 'Rcpp', 'withr'

Packages suggested but not available for checking:
  'testthat', 'monitoR', 'tuneR', 'knitr', 'rmarkdown', 'stringr',
  'numbers', 'purrr', 'scales', 'httr', 'viridis', 'av'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'torch', 'fs', 'zip', 'pins', 'torchvision', 'stringr', 'withr'

Packages suggested but not available for checking:
  'testthat', 'readr', 'coro', 'tokenizers'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'R6', 'withr', 'rlang', 'bit64', 'magrittr', 'coro', 'callr',
  'cli', 'ellipsis'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'glue', 'palmerpenguins',
  'mvtnorm', 'numDeriv', 'katex'

VignetteBuilder 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', 'torch', 'rlang', '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:
  'torch', 'fs', 'rlang', 'rappdirs', 'jpeg', 'png', 'abind', 'withr'

Packages suggested but not available for checking:
  'testthat', 'magick', 'coro', 'zip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'ggplot2', 'scales', 'gridExtra'

Packages suggested but not available for checking:
  'testthat', 'covr', 'caret', 'glmnet', 'randomForest', 'knitr',
  'rmarkdown'

VignetteBuilder 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', 'readr', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tm', 'lda', 'quanteda', 'lubridate', 'htmltools', 'RColorBrewer',
  'stringr', 'WikipediR', 'data.table'

Packages suggested but not available for checking:
  'toscaData', 'testthat', 'knitr', 'devtools', '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'
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: 'Formula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bibliometrix', 'igraph', 'CINNA', 'dplyr', 'rebus', 'magrittr',
  'stringr', 'tidyr', 'rlang', 'tibble'

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:
  'jmvcore', 'ggplot2', 'R6', 'ggdist', 'distributional', 'cowplot',
  'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'broom', 'car', 'afex', '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', 'data.table', 'magrittr', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TreeTools'

Packages suggested but not available for checking: 'ape', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nleqslv', 'numDeriv', 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'engsoccerdata'
'LazyData' is specified without a 'data' directory
Running examples in 'TouRnament-Ex.R' failed
The error most likely occurred in:

> ### Name: leaguetable
> ### Title: Create a league table
> ### Aliases: leaguetable
> 
> ### ** Examples
> 
> #league table for La Liga 94/95 with three point rewards (instead of two) and home and away results
> require(engsoccerdata)
Loading required package: engsoccerdata
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'engsoccerdata'
> leaguetable(dataset=engsoccerdata::spain[which(engsoccerdata::spain$Season==1994),],
+ home="home", away="visitor",score_home="hgoal", score_away="vgoal", date="Date",
+ points = c(3,1,0), rank_by = c("Pts_DC","GD_DC","GF_DC","GD","GF"), DC_display = TRUE)
Error in loadNamespace(x) : there is no package called 'engsoccerdata'
Calls: leaguetable ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'TeachingDemos', 'ash', 'energy', 'testthat', 'colorspace',
  'ggplot2', 'gifski', 'geozoo', 'knitr', 'rmarkdown', '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:
  'dplyr', 'tidyr', 'DT', 'leaflet', 'ggplot2', 'magrittr', 'shiny',
  'shinydashboard', 'RColorBrewer', 'readxl', 'shinyAce',
  'shinycssloaders'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'knitr', 'here', 'tcpl', 'openxlsx', '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:
  'S4Vectors', 'rlang', 'BiocGenerics', 'pryr', 'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', 'covr', 'DBI'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Package required but not available: 'pROC'

Packages suggested but not available 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', 'ks', 'gridExtra', 'mvtnorm'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MESS', 'foreach', 'XML', 'RCurl', 'igraph'

Packages suggested but not available for checking: 'geeM', 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'knitr', 'xlsx', 'readxl'

Packages suggested but not available for checking: 'rmarkdown', 'openxlsx'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'assertthat', 'magrittr', 'dplyr', 'purrr', 'stringr',
  'tidyr', 'tidyselect', 'tibble', 'lifecycle', 'forcats'

Packages suggested but not available for checking:
  'testthat', 'haven', 'knitr', 'rmarkdown', 'huxtable', 'tidyverse',
  'readr', 'kableExtra', 'pharmaRTF', 'withr'

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'

Packages which this enhances but not available for checking:
  'p3state.msm', 'etm'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/TPmsm.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/TPmsm.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'pracma', 'skewMLRM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lgtdl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RCurl', 'XML', 'dplyr', 'plyr', 'reshape', 'rappdirs', 'readxl',
  'shiny', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quadprog', 'glmnet', 'keras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jsonlite', 'Rcpp', 'testit'

Packages suggested but not available for checking:
  'ape', 'ggplot2', 'hunspell', 'knitr', 'markdown', 'phangorn',
  'rappdirs', 'rbenchmark', 'reshape2', 'rmarkdown', 'spelling',
  '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: 'clisymbols', 'crayon', 'prettycode'

Packages suggested but not available for checking:
  'covr', 'mockery', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tgram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'adehabitatHR', 'dplyr', 'foreach', 'geosphere', 'ggplot2',
  'lubridate', 'magrittr', 'maptools', 'purrr', 'raster', 'rlang',
  'sf', 'sp', 'tidyr'

Packages suggested but not available for checking:
  'adehabitatLT', 'doParallel', 'knitr', 'maps', 'Matching', 'move',
  'rmarkdown', 'tinytest', 'rgeos', '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:
  'png', 'neuralnet', 'raster', 'Rcpp', 'shiny', '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:
  'tibble', 'data.table', 'sp', 'lubridate'

Packages suggested but not available for checking:
  'readr', 'dplyr', 'ggplot2', 'knitr', 'rmarkdown', 'adehabitatLT',
  'move', 'moveVis', 'ctmm', 'moveHMM', '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: 'cli', 'googledrive', 'rmarkdown'

Packages suggested but not available for checking:
  'covr', 'devtools', 'gargle', 'knitr', 'pagedown', 'sodium',
  'testthat', '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:
  'trackeR', 'colorspace', 'zoo', 'foreach', 'plotly', 'DT',
  'changepoint', 'shiny', 'shinyjs', 'shinydashboard', 'shinyWidgets',
  'sf', 'mapdeck', 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'ggplot2', 'ggridges', 'xml2', 'RSQLite', 'jsonlite',
  'raster', 'scam', 'foreach', 'fda', 'sp', 'leaflet', 'ggmap',
  'gridExtra', 'gtable'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'scriptests'
Packages unavailable to check Rd xrefs: 'g.data', 'filehash'
Packages required but not available: 'fields', 'RColorBrewer'

Packages suggested but not available for checking:
  'onion', 'plotrix', 'rgl', 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'EBImage', 'data.table', 'dplyr', 'Momocs', 'raster', 'zoo', 'plyr',
  'pastecs', 'features', 'jpeg', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'animation'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ore', 'reportr', 'shades', 'RNifti'

Packages suggested but not available for checking:
  'mmand', 'loder', 'divest', 'jsonlite', 'yaml', 'testthat'

Package which this enhances but not available for checking: 'oro.nifti'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'tibble', 'ggplot2', 'dplyr', 'tidyr', 'purrr', 'cli',
  'crayon', 'sandwich', 'lmtest', 'broom', 'msm', 'rstudioapi'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'antitrust'

Packages suggested but not available for checking:
  'BB', 'competitiontoolbox', 'rmarkdown', 'bookdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'memoise', 'data.table', 'digest'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tibble', 'testthat', 'vcr', 'covr', 'arrow'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'reticulate', 'PerformanceAnalytics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FNN', 'moments', 'pryr', 'lmtest'

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:
  'neuralnet', 'xgboost', 'randomForest', 'e1071', 'kknn', 'dplyr',
  'ada', 'dummies', 'stringr', 'adabag', 'glmnet', 'ROCR', 'ggplot2',
  'scales', 'glue'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rpart.plot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RCurl', 'dplyr', 'glue', 'lubridate', 'magrittr', 'purrr',
  'stringr', 'tibble', 'tidyr', 'usethis', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'geodist', 'geosphere'

Packages suggested but not available for checking:
  'covr', 'testthat', 'dplyr', 'tibble', 'tidyr', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'reshape2', 'taxize', 'getPass', 'units', 'suppdata',
  'curl', 'XML', 'RCurl', 'plyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'httr', 'crul', 'tibble', 'data.table', 'readr',
  'taxize', 'xml2', 'rvest', 'hoardr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'dplyr', '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: 'rlist', 'gridExtra', 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'trajectories', 'xts', 'spacetime', 'RPostgreSQL', 'geosphere',
  'rgdal'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'ggplot2', 'rgeos',
  '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: 'sp', 'spacetime', 'zoo'

Packages suggested but not available for checking:
  'rgdal', 'rgeos', 'OpenStreetMap', 'RCurl', 'rjson', 'adehabitatLT',
  'xts', 'knitr', 'rgl', 'forecast', 'spatstat', 'spatstat.core',
  'spatstat.geom', 'taxidata'

VignetteBuilder 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', 'numDeriv', 'ucminf', 'capushe',
  'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'psych', 'pastecs', 'NbClust', 'GPArotation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'signal', 'plotrix'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'BH', 'readr', 'sp'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TraMineR', 'gtools', 'RColorBrewer', 'colorspace', 'doParallel',
  'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colorspace', 'RColorBrewer', 'weights', 'cNORM'

Packages suggested but not available for checking:
  'xtable', 'TraMineRextras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tram', 'mlt', 'alabama', 'lme4', 'TMB', 'variables', 'basefun',
  'mvtnorm', 'numDeriv', 'coneproj', 'RcppEigen'

Packages suggested but not available for checking:
  'multcomp', 'knitr', 'coxme', 'ordinal', 'ordinalCont', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/tramME.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tram', 'CVXR', 'mlrMBO', 'mlt', 'basefun', 'sandwich',
  'ParamHelpers', 'lhs', 'mlr', 'smoof'

Packages suggested but not available for checking:
  'penalized', 'TH.data', 'knitr', 'mlbench', 'colorspace', 'mvtnorm',
  'glmnet', 'trtf', 'lasso2', 'kableExtra', 'coin', 'tbm',
  'DiceKriging'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/tramnet.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coro', 'fastmap', 'rlang'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'bench', 'testthat', '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:
  'mlt', 'Formula', 'multcomp', 'variables', 'basefun', 'sandwich'

Packages suggested but not available for checking:
  'TH.data', 'trtf', 'mlbench', 'knitr', 'quantreg', 'colorspace',
  'ATR', 'lme4', 'merDeriv', 'SparseGrid', 'alabama', 'numDeriv',
  'gridExtra', 'latticeExtra', 'HSAUR3', 'mvtnorm', 'ordinalCont',
  'coxme', 'glmmsr', 'mlt.docreg', 'ordinal', 'coin', 'asht'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mtram.Rnw'
   'inst/doc/tram.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

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: 'reticulate', 'pbapply'

Packages suggested but not available for checking:
  'markdown', '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:
  'Rcpp', 'tweenr', 'rlang', 'sf', 'lpSolve'

Package suggested but not available for checking: 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stars', 'sf', 'doParallel', 'foreach', 'units', '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: 'RJSONIO', 'RCurl', 'textcat', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'statmod', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cmna', 'ggformula', 'ggplot2', 'plot3D'

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', 'ape'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'purrr', 'coda', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'stringr', 'knitr', 'rmarkdown', 'testthat', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'transplantr-Ex.R' failed
The error most likely occurred in:

> ### Name: chi2dob
> ### Title: Convert CHI number to date of birth
> ### Aliases: chi2dob
> 
> ### ** Examples
> 
> # as a single numeric
> chi2dob(1503541234)
Error: The stringr package is needed for this function to work. Please install it.
Execution halted
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'data.table', 'RcppEigen'

Packages suggested but not available for checking:
  'animation', 'ks', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rootSolve', 'truncSP', 'SQUAREM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rlang'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'cli', 'testthat', 'knitr', 'DescTools',
  'outliers', 'rmarkdown', 'mFilter', '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: 'ggplot2', 'plyr'
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Errors in running code in vignettes:
when running code in 'trapezoid.Rnw'

> options(width = 70)

> options(continue = " ")

> require(trapezoid)
Loading required package: trapezoid

> require(plyr)
Loading required package: plyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'plyr'

> require(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'

> x <- seq(from = 0, to = 1, by = 0.01)

> density <- dtrapezoid(x, min = 0, mode1 = 1/3, mode2 = 2/3, 
+     max = 1, n1 = 2, n3 = 2, alpha = 1)

> trapezoid <- ggplot(data = data.frame(x, density), 
+     aes(x = x, y = density)) + geom_line() + theme_bw()

  When sourcing 'trapezoid.R':
Error: could not find function "ggplot"
Execution halted

  'trapezoid.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'trapezoid.Rnw' using Sweave
Loading required package: trapezoid
Loading required package: plyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'plyr'
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'

Error: processing vignette 'trapezoid.Rnw' failed with diagnostics:
 chunk 2 (label = trapezoid) 
Error in ggplot(data = data.frame(x, density), aes(x = x, y = density)) : 
  could not find function "ggplot"

--- failed re-building 'trapezoid.Rnw'

SUMMARY: processing the following file failed:
  'trapezoid.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'crayon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DEoptim', 'ggplot2', 'ggpubr', 'rootSolve', 'Runuran', 'squash',
  'TSA'

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: 'Rlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quantmod', 'zoo', 'dplyr', 'xts', 'lubridate'

Packages suggested but not available for checking:
  'PerformanceAnalytics', 'tidyr', 'ggplot2', 'dataseries', 'knitr',
  'rmarkdown'

VignetteBuilder 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', 'binom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'memoise'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'XML', 'RCurl', '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:
  'Rcpp', 'runjags', 'coda', 'rjags', 'hypergeo', 'logspline',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'abind', 'plyr', 'ggplot2', 'lmtest', 'lmodel2', 'np',
  '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: 'plyr'

Packages suggested but not available for checking: 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sparseLDA', 'mvtnorm', 'reshape2', 'gtable', 'phyloseq', 'ggplot2',
  'ape'

Packages suggested but not available for checking:
  'adaptiveGPCA', 'knitr', 'testthat', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lazyeval', 'ape', 'geiger', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'limSolve'

Packages suggested but not available for checking:
  'lubridate', 'ggplot2', 'foreach', 'iterators', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lubridate', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ape', 'cowplot', 'tree', '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:
  'mlpack', 'fitdistrplus', 'igraph', 'nFactors', 'Rcpp',
  'RColorBrewer', 'Rdpack'

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', 'cli', 'colorspace', 'memoise', 'phangorn', 'Rdpack', 'shiny',
  'shinyjs', 'TreeTools', 'Rcpp'

Packages suggested but not available for checking:
  'bookdown', 'ggplot2', 'hypervolume', 'kdensity', 'knitr',
  'protoclust', 'Quartet', 'readxl', 'rmarkdown', 'Rcpp', 'rgl',
  'spelling', 'testthat', 'Ternary', 'TreeDistData', 'TreeSearch',
  'Umatrix', 'uwot', '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:
  'ape', 'Rcpp', 'apTreeshape', '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:
  'ggplot2', 'igraph', 'patchwork', 'pracma'

Packages suggested but not available for checking:
  'Seurat', 'gridExtra', 'knitr', 'plotly', 'qpdf', '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:
  'ggparty', 'ggplot2', 'partykit', 'dplyr', 'ggnewscale', 'gtable',
  'tidyr', 'yardstick', 'seriation'

Packages suggested but not available for checking:
  'forcats', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'randomForest', 'ranger', 'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Build_JTree: no visible global function definition for 'flush.console'
Run_JTree: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Packages required but not available:
  'plyr', 'ape', 'RJSONIO', 'stringr', 'bigmemory'

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', 'ggfittext'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'vdiffr', '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:
  'colorspace', 'data.table', 'ggplot2', 'gridBase', 'igraph',
  'RColorBrewer', 'shiny'

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:
  'Rcpp', 'ape', 'RcppArmadillo', 'RcppThread'

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: 'ape', 'subplex', 'TreeSim', 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'dplyr', 'Rcpp', 'lazyeval', 'phytools', 'geiger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'cli', 'fastmatch', 'future', 'promises', 'protoclust',
  'Rcpp', 'Rdpack', 'Rogue', 'shiny', 'shinyjs', 'TreeDist',
  'TreeTools'

Packages suggested but not available for checking:
  'knitr', 'phangorn', 'Quartet', 'rmarkdown', 'shinytest', 'spelling',
  '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: 'TreeSim', 'ape'

Packages suggested but not available 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', 'geiger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'ade4', 'adegenet', 'adegraphics', 'adephylo', 'combinat',
  'distory', 'fields', 'htmlwidgets', 'phangorn', 'phytools', 'Rcpp',
  'rgl', 'RLumShiny', 'scatterD3', 'shiny', 'shinyBS'

Packages suggested but not available for checking:
  'ggplot2', 'igraph', 'knitr', 'pander', 'RColorBrewer', '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: 'phytools', 'ape'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'Rcpp'

Packages suggested but not available for checking:
  'ggtree', 'ggplot2', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'bit64', 'lifecycle', 'colorspace', 'fastmatch', 'R.cache',
  'Rdpack', 'Rcpp'

Packages suggested but not available for checking:
  'spelling', 'knitr', 'phangorn', 'Rcpp', 'rmarkdown', '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:
  'shiny', 'RColorBrewer', 'spatstat.geom', 'spatstat.core', 'raster',
  'rasterVis', 'sp', 'geometry', 'rgdal', 'rgeos', 'rgl', 'lidR',
  'pryr', 'sf', 'stars'

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:
  'testthat', 'knitr', 'rmarkdown', 'covr'

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:
  'dplyr', 'purrr', 'htmltools', 'DistributionUtils', 'gtable',
  'digest', 'jsonlite', 'ggplot2', 'base64enc', 'htmlwidgets',
  'progress', 'knitr', 'webshot', 'autocogs', 'tidyr', 'rlang'

Packages suggested but not available for checking:
  'plotly', 'testthat', 'covr', 'gapminder', 'rmarkdown', 'shiny',
  'housingData'

VignetteBuilder 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', '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: 'cli', 'crayon', 'crul', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'clipr', 'vcr', '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:
  'testthat', 'knitr', 'rmarkdown', '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:
  'trending', 'yardstick', 'rsample', 'ellipsis', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'outbreaks'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'vctrs', 'ciTools'

Packages suggested but not available for checking:
  'brms', 'covr', 'ggplot2', 'knitr', 'outbreaks', 'patchwork',
  'rmarkdown', 'dplyr', '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: 'pROC', 'rms', 'nleqslv', 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'extraDistr'

Packages suggested but not available for checking:
  'strucchange', 'Kendall', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'changepoint', 'forecast', 'plyr', 'Rssa', 'tseries', 'zoo',
  'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gtrendsR', 'magrittr', 'dplyr', 'purrr', 'crayon', 'stringr',
  'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ManifoldOptim', 'pracma', 'rTensor'

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', 'zoo', 'solaR', 'lubridate', 'lhs', 'doParallel', 'foreach',
  'tibble', 'dplyr', 'sensitivity', 'randtoolbox', 'doSNOW', 'msm',
  'magrittr'

Packages suggested but not available for checking: 'shiny', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'snpStats', 'foreach', '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:
  'Rcpp', 'rstan', 'rstantools', 'rlang', 'dplyr', 'purrr', 'magrittr',
  'stringr', 'ggplot2', 'gtools', 'coda', 'tidybayes', 'tibble',
  'binom', 'StanHeaders', 'BH', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyr', 'ggridges', 'DiagrammeR'

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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rlang', 'vctrs', 'cpp11'

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', 'lazyeval', 'magrittr', 'rlang', 'rstudioapi'

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:
  'ggplot2', 'ggtern', 'shiny', 'assertthat'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'sf', 'leaflet', 'httpuv', '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:
  'loo', 'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'dplyr',
  'future', 'glue', 'purrr', 'tidyr', 'Formula', 'bayesplot', 'BH',
  'RcppEigen', 'StanHeaders'

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: '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: 'sf', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'scales', 'reshape2', 'ez', 'psych', 'PSAgraphics',
  'gridExtra', 'randomForest'

Package suggested but not available for checking: 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fpc'
Package unavailable to check Rd xrefs: 'fpc'
Packages required but not available: 'data.table', 'crayon', 'cli', 'pryr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'randomForest', 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rgl', 'gridExtra'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'reshape'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'msm', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'akima'
Packages required but not available: 'rgdal', 'sp', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'plyr'

Package suggested but not available for checking: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'DALEX', 'glmnet', 'ggdendro', 'patchwork'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'randomForest', 'mlbench', 'ranger', 'gbm',
  'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geodist', 'raster', 'reproj', 'sp', 'spatstat.geom',
  'spatstat.core', 'glue', 'viridis', 'traipse', 'crsmeta', 'dplyr',
  'rlang'

Packages suggested but not available for checking:
  'adehabitatLT', 'knitr', 'testthat', 'covr', 'rmarkdown',
  'lubridate', 'maps', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'data.tree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'limSolve', 'generics'

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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'magrittr', 'dplyr', 'tibble', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'spelling', 'knitr', 'rmarkdown', 'viridis', 'ggplot2',
  'countrycode', 'tidyr', 'stringr', 'readstata13', 'haven', 'maps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'msm', 'reshape2', 'GenSA', 'GA', 'doParallel'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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:
  'coda', 'data.table', 'ggplot2', 'gridExtra', 'hdrcde', 'MCMCglmm',
  'plyr', 'rjags'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Packages required but not available:
  'mlt', 'partykit', 'Formula', 'sandwich', 'variables', 'libcoin'

Packages suggested but not available for checking: 'TH.data', 'coin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'hdrcde'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'purrr', 'tidyr'

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.
DrawMargin: no visible global function definition for 'qnorm'
DrawProbability: no visible global function definition for 'pnorm'
Factor: no visible global function definition for 'new'
Gaussian: no visible global function definition for 'new'
LikelihoodFactor: no visible global function definition for 'new'
Parameters: no visible global function definition for 'new'
Player: no visible global function definition for 'new'
PriorFactor: no visible global function definition for 'new'
SumFactor: no visible global function definition for 'new'
TruncateFactor: no visible global function definition for 'new'
Variable: no visible global function definition for 'new'
Vdraw: no visible global function definition for 'dnorm'
Vdraw: no visible global function definition for 'pnorm'
Vwin: no visible global function definition for 'dnorm'
Vwin: no visible global function definition for 'pnorm'
Wdraw: no visible global function definition for 'dnorm'
Wdraw: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'hash'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rfast', 'doParallel', 'foreach', 'iterators', 'fpc'

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:
  'nleqslv', 'randtoolbox', 'alabama', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mvtnorm', 'testthat', 'carData'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'evd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'invgamma', 'rmutil'

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 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.
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Package suggested but not available for checking: 'testthat'
Package required but not available: 'maxLik'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'truncreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'digest', 'jsonlite', 'httr'

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'

VignetteBuilder 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', 'data.table', 'rvest'

Package suggested but not available for checking: 'R.utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ordinal', 'magrittr', 'dplyr', 'tibble', 'tidyr', 'lme4', 'readr',
  'purrr', 'rmarkdown', 'emmeans', 'DT', 'Rdpack', 'ggplot2',
  'forcats', 'ez'

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:
  'futile.logger', 'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'futile.logger'
Running 'testthat.R'
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: 'forecast', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'vars', 'fftwtools', 'hdm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaps', 'locfit', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'anytime'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble', 'forecast', 'seasonal', 'dygraphs',
  'xts', 'ggplot2', 'scales', 'knitr', 'rmarkdown', 'tsibble',
  'tsibbledata', 'tibbletime', 'tseries', 'zoo', 'tis', 'timeSeries',
  'nycflights13', 'imputeTS', '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:
  'ICtest', 'JADE', 'BSSprep', 'Rcpp', 'forecast', 'xts', 'zoo',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'stochvol', 'MTS', 'tsbox', 'dr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pdc', 'locpol', 'dtw', 'longitudinalData', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'TSdbi', 'tframe', 'tfplot', 'DBI'

Packages suggested but not available for checking:
  'tframePlus', 'TSsql', 'TSMySQL', 'TSSQLite', 'TSmisc', 'zoo'

Packages which this enhances but not available for checking:
  'TSPostgreSQL', 'TSodbc', 'TSfame'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'xts', 'FKF', 'ltsa', 'rvinecopulib', 'FitAR', 'arfima'

Packages suggested but not available 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: 'ltsa'

Packages suggested but not available for checking:
  'xtable', 'gamlss.data', 'surveillance'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Qhat: no visible global function definition for 'pnorm'
plrt: no visible global function definition for 'uniroot'
plrt: no visible global function definition for 'optimize'
simulatedata: no visible global function definition for 'rnorm'
tsc.test: no visible global function definition for 'shapiro.test'
tsc.test: no visible global function definition for 'p.adjust'
tsc.test: no visible global function definition for 'glm'
tsc.test : f: no visible global function definition for 'pnorm'
tsc.test: no visible global function definition for 'uniroot'
tsc.test: no visible global function definition for 'optimize'
variance: no visible global function definition for 'density'
variance: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'tseries', 'rgl'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tframe', 'tframePlus', 'tfplot', 'TSdbi', 'TSsql', 'TSPostgreSQL',
  'TSMySQL', 'TSSQLite', 'TSodbc', 'TSsdmx', 'TSmisc', 'TScompare',
  'zoo', 'xts', 'tseries', 'WriteXLS', 'DBI', 'RPostgreSQL', 'RSQLite',
  'RMySQL', 'RODBC', 'RJSDMX'
Packages unavailable to check Rd xrefs: 'TSdbi', 'TSPostgreSQL', 'TSMySQL', 'TSSQLite', 'TSodbc', 'TSsdmx', 'TSmisc', 'TScompare', 'tframe', 'tfplot', 'zoo', 'xts', 'tseries', 'WriteXLS', 'DBI', 'RJSDMX', 'RPostgreSQL', 'RSQLite', 'RMySQL', 'RODBC'
Packages required but not available: 'DBI', 'tframe'

Packages suggested but not available for checking:
  'zoo', 'tseries', 'tis', 'tfplot', 'tframePlus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'datetimeutils', 'fastmatch', 'zoo'

Packages suggested but not available for checking: 'data.table', 'tinytest'

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.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
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:
  'proxy', 'dtw', 'locpol', 'longitudinalData', 'pdc', 'TSclust',
  'xts', '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:
  'mlbench', 'hash', 'party', 'survRM2', 'modeltools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mnormt', 'tseriesChaos', 'tseries', 'vars', 'urca', 'forecast',
  'foreach'

Packages suggested but not available for checking:
  'sm', 'scatterplot3d', 'rgl', 'tidyverse', 'rugarch'

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: 'stats'
  All declared Imports should be used.
Packages required but not available:
  'xts', 'zoo', 'RcppRoll', 'ranger', 'glmnet', 'earth', 'kernlab',
  'Cubist', 'gbm', 'pls', 'monmlp', 'doParallel', 'foreach', 'xgboost',
  'softImpute'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'wordcloud', 'wordcloud2', 'ggplot2', 'httr', 'syuzhet',
  'tidytext', 'dplyr', 'tibble', 'progress', 'stringi'

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: 'knitr', 'rmarkdown'
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Package required but not available: 'deSolve'

Package suggested but not available for checking: 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cubature', 'ks'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'quadprog', 'zoo', 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'quantmod', 'quadprog'

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: 'stats'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'ggplot2', 'gridExtra', 'mvtnorm'
Running examples in 'ts.extend-Ex.R' failed
The error most likely occurred in:

> ### Name: dGARMA
> ### Title: Density function for the stationary GARMA distribution
> ### Aliases: dGARMA
> 
> ### ** Examples
> 
> data(garma)
> AR <- c(0.8, -0.2)
> MA <- c(0.6,  0.3)
> 
> #Compute the density of the GARMA output
> (DENSITY <- dGARMA(SERIES, ar = AR, ma = MA))
Error in loadNamespace(x) : there is no package called 'mvtnorm'
Calls: dGARMA ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'TSdbi', 'DBI', 'tframe', 'tframePlus', 'fame', 'tis'

Packages suggested but not available for checking:
  'tseries', 'tfplot', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fracdiff', 'forecast', 'purrr', 'RcppRoll', 'tibble', 'tseries',
  'urca', 'future', 'furrr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'tidyr', 'dplyr',
  'Mcomp', 'GGally'

VignetteBuilder 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'

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', '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: 'fracdiff', 'forecast'

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:
  'caret', 'edgeR', 'fastmatch', 'genalg', 'kernlab', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tcltk2', 'tkrplot', 'RandomFieldsUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tsibble', 'rappdirs'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'anytime', 'dplyr', 'ellipsis', 'generics', 'lifecycle', 'lubridate',
  'rlang', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'hms', 'knitr', 'nanotime', 'nycflights13',
  'rmarkdown', 'scales', 'spelling', 'testthat', 'tidyr', 'timeDate'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crosstalk', 'dendextend', 'dplyr', 'glue', 'lubridate', 'plotly',
  'R6', 'rlang', 'shiny', 'tsibble', 'vctrs'

Packages suggested but not available for checking: 'fabletools', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MAPA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'kernlab', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'keras', 'tensorflow', 'tsutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plus', 'lars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'ggplot2', 'plyr', 'reshape2'

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:
  'TSdbi', 'DBI', 'tframe', 'tframePlus', 'zoo', 'tseries', 'quantmod',
  'gdata'

Packages suggested but not available for checking:
  'tfplot', 'xts', 'timeSeries', 'tis'

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: 'gam'
Malformed Description field: should contain one or more complete sentences.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
Packages required but not available:
  'audio', 'checkmate', 'doSNOW', 'foreach', 'magrittr', 'progress',
  'Rcpp', 'RcppParallel', 'RJSONIO'

Packages suggested but not available for checking:
  'covr', 'gdtools', 'knitr', 'rmarkdown', 'raster', 'spelling',
  '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:
  'sn', 'mvtnorm', 'numDeriv', 'progress'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TSdbi', 'DBI', 'tframe', 'TSsql', 'RMySQL'

Packages suggested but not available for checking:
  'zoo', 'tseries', 'tfplot', 'tframePlus', 'timeSeries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'network', 'networkDynamic', 'statnet.common'

Packages suggested but not available for checking:
  'networkDynamicData', 'testthat', 'sna', 'knitr', 'rmarkdown',
  'relevent', 'ergm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TSdbi', 'DBI', 'tframe', 'tframePlus', 'TSsql', 'RODBC'

Packages suggested but not available for checking:
  'zoo', 'tseries', 'tfplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glasso', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'KFAS'

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', 'TSP', 'BBmisc', 'checkmate', 'fpc', 'vegan', 'stringr',
  'splancs'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TSdbi', 'DBI', 'tframe', 'tframePlus', 'TSsql', 'RPostgreSQL'

Packages suggested but not available for checking:
  'zoo', 'tseries', 'tfplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'foreach'

Packages suggested but not available for checking:
  'sp', 'maps', 'maptools', 'doParallel', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forecast', 'KFAS', 'MuMIn', 'EMD', 'wavelets', 'vars',
  'ModelMetrics', 'RSNNS', 'Rlibeemd', 'e1071', 'elmNNRcpp',
  'randomForest', 'magrittr', 'plyr', 'dplyr', 'keras', 'tfdatasets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'robustbase', 'fracdiff'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'quantreg', 'wavelets', 'dtt'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'data.table', 'moments', '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:
  'glmnet', 'mclust', 'quantreg', 'Rdpack', 'textTinyR', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TSdbi', 'DBI', 'tframe', 'tframePlus', 'RJSDMX', 'rJava'

Package suggested but not available for checking: 'tfplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xts', 'zoo', 'timeDate', 'dsa', 'tsbox'

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:
  'TSdbi', 'DBI', 'tframe', 'tframePlus', 'TSsql', 'RSQLite'

Packages suggested but not available for checking:
  'zoo', 'tseries', 'tfplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'tframe', 'TSdbi', 'tframePlus', 'zoo'

Packages suggested but not available for checking:
  'tseries', 'tis', 'tfplot', 'RMySQL', 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bfast', 'broom', 'strucchange', 'ggplot2', 'RcppRoll', 'mblm'

Packages suggested but not available for checking: 'rgl', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'forecast', 'forecastHybrid', 'future',
  'future.apply', 'lubridate', 'magrittr', 'plotly', 'purrr',
  'RColorBrewer', 'reshape2', 'scales', 'tidyr', 'tsibble', 'viridis',
  'xts', 'zoo'

Packages suggested but not available for checking:
  'devtools', 'DT', 'knitr', 'quantmod', 'rmarkdown', 'UKgrid'

VignetteBuilder 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', 'stringdist', 'data.table'

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:
  'RColorBrewer', 'forecast', 'MAPA', 'plotrix'

Package suggested but not available for checking: 'thief'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotrix'

Package suggested but not available for checking: 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'plotly', 'shiny', 'miniUI', 'forecast',
  'ggplot2', 'magrittr', 'shinyhelper'

Packages suggested but not available for checking: 'testthat', 'lintr'

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', 'vdiffr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Running 'testthat.R'
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:
  'signal', 'PolynomF', 'waveslim', 'astsa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'evd', 'mvtnorm', 'tictoc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pastecs', 'reshape', 'e1071', 'relimp', 'multcomp', 'rkt',
  'stlplus', 'tcltk2', 'mvtnorm', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.core', 'spatstat.random',
  'spatstat.linnet', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quantreg', 'tcltk2', 'RISmed', 'VennDiagram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tinytest', 'diffobj'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/r_packages/pkgcheck/CRAN/tth/tth.Rcheck/00install.out' for details.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'latticeExtra'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown', '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:
  'DT', 'dplyr', 'magrittr', 'purrr', 'data.tree', 'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'zoo', 'curl'

Package suggested but not available for checking: 'RUnit'

Package which this enhances but not available for checking: 'quantmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixStats', 'sva', 'limma', 'corpcor', 'simsalapar'

Package suggested but not available for checking: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package required but not available: 'sfsmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rTensor', 'tensorr', 'PTAk'

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', 'knitr', 'htmltools'

Packages suggested but not available for checking:
  'rmarkdown', 'table1', 'magrittr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.saveDevice: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
Package required but not available: 'data.table'

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', 'testthat', 'rmarkdown', '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:
  'httr', 'plyr', 'dplyr', 'purrr', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'xml2', 'lintr', 'hms'

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', '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:
  'raster', 'readr', 'tibble', 'tidyr', 'stringr', 'rgdal', 'sp',
  'dplyr', 'gstat', 'lubridate', 'ggplot2', 'rlang', 'magrittr'

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: 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rmarkdown', 'knitr'

Packages suggested but not available for checking: '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: 'doBy', 'xtable'

Packages suggested but not available for checking: 'pbkrtest', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'minqa', 'Rdpack', 'rootSolve'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgl', 'ddalpha', 'bfp', 'Rglpk', 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'multcomp', 'pbkrtest', 'lme4'

Packages suggested but not available for checking:
  'knitr', 'xtable', 'reshape2', 'sandwich', 'CorrBin', 'SASmixed',
  'SimComp', 'HSAUR3'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/ExamplesTukeytrendtest.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tensr', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'RCurl', 'stringr', 'RJSONIO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'minpack.lm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'snowfall', 'desire', 'igraph', 'gsl', 'tree', 'e1071',
  'randomForest', 'klaR'
Packages unavailable to check Rd xrefs: 'igraph', 'e1071', 'tree', 'randomForest', 'klaR', 'desire'
Running examples in 'TunePareto-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.TuneParetoModel
> ### Title: Prediction method for TuneParetoClassifier objects
> ### Aliases: predict.TuneParetoModel
> ### Keywords: prediction
> 
> ### ** Examples
> 
> # train an SVM classifier
> cl <- tunePareto.svm()
Loading required package: e1071
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'e1071'
> tr <- trainTuneParetoClassifier(cl, 
+                                 iris[,-ncol(iris)], 
+                                 iris[,ncol(iris)], 
+                                 cost=0.001)
Error in svm(x = list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6,  : 
  could not find function "svm"
Calls: trainTuneParetoClassifier -> do.call
Execution halted
Packages required but not available:
  'ranger', 'mlrMBO', 'lubridate', 'lhs', 'mlr', 'smoof',
  'ParamHelpers', 'BBmisc', 'DiceKriging'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dials', 'dplyr', 'foreach', 'generics', 'ggplot2', 'glue',
  'GPfit', 'hardhat', 'lifecycle', 'parsnip', 'purrr', 'recipes',
  'rlang', 'rsample', 'tibble', 'tidyr', 'vctrs', 'withr', 'workflows',
  'yardstick'

Packages suggested but not available for checking:
  'covr', 'kernlab', 'knitr', 'modeldata', 'spelling', 'testthat',
  'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'signal'

Package suggested but not available for checking: 'pastecs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'numDeriv', 'quantreg', 'iterators'

Package suggested but not available for checking: 'setRNG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tester'

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/turner_introduction.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', 'digest'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/TurtleGraphics.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/TurtleGraphics.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available:
  'httr', 'tidyverse', 'forecast', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'markdown', 'knitr', 'rjson', 'base64enc'

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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'garchx', 'zoo', 'numDeriv', 'hier.part'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggthemes', 'ggplot2', 'dplyr', 'tidyr', 'purrr', 'knitr',
  'rmarkdown', 'magrittr', 'gridExtra', '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: 'dplyr', 'ggplot2', 'kedd', 'locpol'

Packages suggested but not available 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', 'robustbase', 'tcltk2', 'gridExtra', 'DescToolsAddIns'

Package suggested but not available for checking: 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'scales'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'systemfit', 'vars', 'bvarsv', 'plm'

Packages suggested but not available 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', 'Rdpack', '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:
  'ggplot2', 'extrafont', 'scales', 'magick'

Packages suggested but not available for checking:
  'testthat', 'gapminder', 'dplyr', 'spelling', 'cowplot', 'png',
  'glue', 'stringr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'gbm', 'survey', 'xtable'

Packages suggested but not available 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:
  'twang', 'gbm', 'latticeExtra', 'survey'

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:
  'gbm', 'survey', 'xtable', 'latticeExtra', 'MatrixModels',
  'data.table', 'ggplot2', 'xgboost'

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:
  'xgboost', 'data.table', 'ggplot2', 'MatrixModels'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

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: 'stabledist', 'statmod'
Package unavailable to check Rd xrefs: 'statmod'
Running examples in 'tweedie-Ex.R' failed
The error most likely occurred in:

> ### Name: AICtweedie
> ### Title: Tweedie Distributions
> ### Aliases: AICtweedie
> ### Keywords: models
> 
> ### ** Examples
> 
> library(statmod) # Needed to use  tweedie  family object
Error in library(statmod) : there is no package called 'statmod'
Execution halted
Packages required but not available: 'Rcpp', 'farver', 'magrittr', 'rlang'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crayon', 'R6', 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'purrr', 'httr', 'jsonlite', 'magrittr', '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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'plyr', 'stopwords', 'stringr', 'dplyr', 'readr',
  'magrittr', 'rtweet', 'quanteda', 'quanteda.textstats',
  'topicmodels', 'stm', 'tidyr', 'rlang', 'maps', 'LDAvis', 'leaflet',
  'ldatuning', 'stringi', 'tm'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'tidytext', 'modeltools', 'servr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'dplyr', 'jsonlite', 'lubridate', 'plyr', 'purrr', 'tibble',
  'twitteR', 'naptime', 'tidytext', 'magrittr'

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: 'bit64', 'rjson', 'DBI', 'httr'

Packages suggested but not available for checking: 'RSQLite', 'RMySQL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'MCMCpack', 'corrplot', 'Rfast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'crayon', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'tidyr', '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: 'blockrand', 'dplyr', 'simsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Packages required but not available:
  'data.table', 'dplyr', 'seewave', '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.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'multcomp', 'glmmTMB', 'pscl', 'pbapply', 'doParallel'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'isotone'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fixest', 'stringr', 'estimatr', 'rlang'

Package suggested but not available for checking: 'wooldridge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'
Packages required but not available:
  'onewaytests', 'ggplot2', 'nortest', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'forcats', 'magrittr', 'rlang', 'knitr'

Packages suggested but not available for checking:
  'testthat', 'lifecycle', 'rmarkdown', 'ggplot2', '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:
  'stringr', 'data.table', 'assertthat', 'mvtnorm', 'hal9001',
  'haldensify', 'lspline', 'ggplot2', 'scales', 'latex2exp', 'Rdpack'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'future', 'future.apply',
  'origami', 'ranger', 'Rsolnp', 'nnls'

Package which this enhances but not available for checking: 'sl3'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'base64url', 'filelock', 'R6'

Packages suggested but not available for checking: 'purrr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'waldo'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringr', 'crayon', 'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'cpp11'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'lifecycle'

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: 'progress', 'V8'

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'sf', 'raster', 'rgdal', 'rgeos', 'geosphere', 'log4r', 'zoo',
  'brew', 'exifr', 'link2GI', 'data.table', 'jsonlite', 'rlist',
  'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'mapview', 'stringr', 'htmltools',
  'htmlwidgets', 'maptools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette rbinom setTxtProgressBar
  txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages required but not available:
  'deSolve', 'dplyr', 'digest', 'doParallel', 'flextable', 'foreach',
  'ggplot2', 'knitr', 'magrittr', 'onbrand', 'optimx', 'PKNCA', 'pso',
  'readxl', 'rmarkdown', 'rhandsontable', 'scales', 'stringr', 'shiny'

Packages suggested but not available for checking:
  'GA', 'GGally', 'gridGraphics', 'gridExtra', 'officer', 'webshot',
  'ggrepel', 'rstudioapi', '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:
  'MBA', 'gstat', 'automap', 'sp', 'randomForest'

Packages suggested but not available for checking:
  'testthat', 'DMwR2', 'ggplot2', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'unmarked', 'ggplot2', 'gridExtra', 'lme4', 'loo', 'pbapply', 'Rcpp',
  'RSpectra', 'rstan', 'rstantools', 'BH', 'RcppArmadillo',
  'RcppEigen', 'StanHeaders', 'RcppParallel'

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'pkgdown', 'raster', 'rmarkdown',
  'rlang', '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: 'ChemmineR', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'knitr', 'stringr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'tinytest', 'knitr', 'rmarkdown', 'curl'

VignetteBuilder package required for checking but not installed: 'knitr'
GNU make is a SystemRequirements.
Packages required but not available:
  'colorspace', 'dplyr', 'geometry', 'pracma', 'ptinpoly', 'rgl',
  'remotes'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dendextend', 'robcor'

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: 'numDeriv'
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:
  'dplyr', 'ezcox', 'forcats', 'ggplot2', 'ggpubr', 'magrittr',
  'ppcor', 'psych', 'purrr', 'shiny', 'stringr', 'tibble', 'tidyr',
  'UCSCXenaTools'

Packages suggested but not available for checking:
  'covr', 'cowplot', 'DT', 'furrr', 'future', 'ggrepel', 'ggstatsplot',
  'knitr', 'pacman', 'plotly', 'plyr', 'RColorBrewer', 'rmarkdown',
  'scales', 'survminer', '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', 'dplyr', 'httr', 'jsonlite', 'magrittr', 'readr', 'rlang'

Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'prettydoc', 'rmarkdown', 'shiny',
  'shinydashboard', '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', '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', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'topicmodels'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'esemifar', 'fracdiff', 'rugarch', 'smoots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'diptest', 'dplyr', 'ggplot2', 'ggrepel', 'ggridges',
  'gridExtra', 'gtable', 'htmltools', 'kableExtra', 'knitr', 'pander',
  'plyr', 'pwr', 'rmdpartials', 'scales', 'SuppDists'

Packages suggested but not available for checking:
  'bootES', 'car', 'careless', 'GGally', 'jmvcore', 'lavaan', 'MBESS',
  'psych', 'rio', 'remotes', 'rmarkdown', 'rstudioapi', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'RMySQL', 'data.table', 'collapse', 'writexl'

Packages suggested but not available for checking:
  'magrittr', 'xts', 'dygraphs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Brobdingnag', 'pbapply', 'gsl'

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', 'gamlss', 'gamlss.dist', 'pracma'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tcltk2', 'tkrplot', 'HMM', 'clValid', 'FactoMineR', 'corrplot',
  'chron'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maxLik', 'mvtnorm', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rmarkdown', 'xaringan'

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:
  'testthat', 'ggplot2', 'dplyr', 'spelling'
Running examples in 'ukbabynames-Ex.R' failed
The error most likely occurred in:

> ### Name: ewbabynames
> ### Title: England & Wales baby names
> ### Aliases: ewbabynames
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'questionr', 'data.table', 'tidyverse', 'magrittr', 'here', '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:
  'data.table', 'dplyr', 'purrr', 'readr', 'ggplot2', 'XML',
  'magrittr', 'tibble', 'tidyr', 'scales', 'stringr', 'foreach',
  '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: 'httr', 'XML'

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:
  'data.table', 'dplyr', 'lubridate', 'magrittr', 'tsibble', 'xts',
  'zoo'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'remotes', 'TSstudio', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'httr', 'jsonlite', 'tibble'

Packages suggested but not available for checking:
  'markdown', 'covr', 'spelling', '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:
  'jsonlite', 'tibble', 'purrr', 'httr', 'snakecase'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'ggplot2', 'dplyr',
  'leaflet', 'htmltools', 'scales', 'sf', '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: 'Rcpp'

Packages suggested but not available for checking:
  'covr', '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: 'coda', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'openssl', 'reticulate', 'Rcpp', 'RSpectra'

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', 'ggplot2', 'shiny', 'shinyjs', 'reshape2', 'fields', 'plyr',
  'png', 'abind', 'deldir', 'geometry', 'pdist', 'AdaptGauss', 'pracma'

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BiocManager', 'dplyr', 'DT', 'forcats', 'ggplot2', 'gridExtra',
  'magrittr', 'pheatmap', 'plotly', 'readr', 'Rsamtools', 'scales',
  'shiny', 'shinydashboard', 'shinyFiles', 'shinyWidgets', 'stringr',
  'tibble', 'tidyr', 'viridis'

Packages suggested but not available 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'
'LazyData' is specified without a 'data' directory
Errors in running code in vignettes:
when running code in 'vignetteUmom.Rnw'
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'vignetteUmom.Rnw' using 'UTF-8'... failed to complete the test
Packages required but not available: 'mc2d', 'BimodalIndex'

Packages suggested but not available for checking:
  'mclust', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'decon', 'trust', 'distr'

Packages suggested but not available for checking: 'purrr', 'Iso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'OpenMx', 'ggplot2', 'cowplot', 'DiagrammeR', 'DiagrammeRsvg',
  'rsvg', 'lavaan', 'MuMIn', 'mvtnorm', 'polycor', 'R2HTML', 'RCurl',
  'scales', 'xtable', 'kableExtra', 'knitr', 'tibble'

Packages suggested but not available for checking:
  'cocor', 'devtools', 'gdata', 'hrbrthemes', 'Hmisc', 'spelling',
  'testthat', 'rmarkdown', 'psych', 'psychTools', 'rhub', 'pwr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'foreach', 'doParallel', 'FNN', 'RANN'

Packages suggested but not available for checking: 'randomForest', 'ROCR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
med: no visible global function definition for 'quantile'
uh: no visible global function definition for 'mad'
uh.bu: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'triangle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pdist', 'kohonen'

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', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'NlcOptim'

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:
  'XML', 'dplyr', 'purrr', 'tidyr', 'tibble', 'Rcpp', 'devtools',
  'usethis', 'R.utils'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'glue', 'testthat', 'rlang', 'covr', 'knitr', 'rmarkdown', 'magrittr'
'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:
  'pbapply', 'Rcpp', 'Rdpack', 'RcppEigen'

Packages suggested but not available for checking:
  'MortalityLaws', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rlang', 'forcats', 'stringr', 'tidyr', 'magrittr',
  'tidyxl', 'readxl', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Iso', 'ahaz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'graph', 'gmp'

Packages suggested but not available for checking:
  'Rgraphviz', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/unifDAG-vignette.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', 'rmarkdown', 'testthat', 'rstan', 'data.table'

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: 'pgnorm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'geometry', 'rgl', 'misc3d', 'scatterplot3d'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'orthopolynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'covr', 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'plyr', 'dplyr', 'scales', 'magrittr', 'magick', 'data.tree',
  'ggplot2', 'tidyverse', 'gridExtra', 'ggpubr', 'curl', 'networkD3',
  'stringr', 'qdapRegex', 'htmlwidgets', 'alakazam', 'gprofiler2',
  'progress', 'ggsci'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Running 'testthat.R'
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:
  'DoseFinding', 'mvtnorm', 'quadprog', 'SEL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'hexView', 'vroom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'easycsv'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'tidyverse', 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'compound.Cox'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

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/unitedR.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crayon', 'diffobj'

Packages suggested but not available 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:
  'NISTunits', 'measurements', 'xml2', 'magrittr', 'pillar', 'dplyr',
  'vctrs', 'ggplot2', 'testthat', 'vdiffr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lmtest'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'extraDistr', 'tibble', 'logitnorm', 'actuar',
  'nakagami', 'fGarch'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'markdown', 'copula', 'dplyr',
  '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:
  'covr', 'nlist', '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: 'robustbase', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'gapminder', 'tidyr', 'testthat', 'covr', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'plyr', 'raster', 'Rcpp', 'TMB', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'data.table', 'dplyr', 'knitr', 'repurrrsive', 'rmarkdown',
  'roxygen2', 'testthat', 'tibble', '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: 'huge', 'PDSCE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'magrittr', 'dplyr', 'forcats', 'purrr', 'tidyr', 'pillar',
  'tibble', 'cellranger', 'xml2', 'tidyselect'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'readr', 'tidyxl', 'readxl', 'stringr',
  'htmltools', 'rvest', 'selectr', 'DT', 'testthat', 'covr', 'here'

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'
'LazyData' is specified without a 'data' directory
Package required but not available: 'sys'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'assertthat', 'lubridate', 'magrittr', 'stringr', 'tibble',
  'tidyr', 'purrr', 'dplyr', 'rlang'

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:
  'Rcpp', 'doParallel', 'foreach', 'iterators', 'RcppArmadillo'

Package suggested but not available for checking: 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Brobdingnag', 'partitions', 'polynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lavaan', 'magrittr', 'dplyr', 'tidyr', 'tibble', 'purrr',
  'simstandard', 'ggplot2', 'ggnormalviolin', 'rlang', 'patchwork',
  'scales', 'ragg', 'lifecycle'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'glue', 'mvtnorm', 'kableExtra', 'forcats',
  'stringr', 'rmarkdown', 'covr', 'roxygen2', 'bookdown'

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', 'dplyr', 'readxl', 'countrycode', 'tidyr', 'lubridate',
  'devtools', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'countrycode'
Note: found 7872 marked UTF-8 strings
Running examples in 'unvotes-Ex.R' failed
The error most likely occurred in:

> ### Name: un_roll_calls
> ### Title: Data on each roll call of the United Nations General Assembly
> ### Aliases: un_roll_calls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Packages required but not available:
  'ltm', 'Rcpp', 'cubature', 'mvtnorm', 'numDeriv', 'statmod',
  'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'assertthat', 'ggplot2', 'ggthemes',
  'reshape2', 'foreach', 'future', 'doFuture', 'doRNG', 'iterators'

Packages suggested but not available for checking:
  'covr', 'testthat', 'SuppDists', 'knitr', 'rmarkdown',
  'VariantAnnotation', 'GenomicRanges', 'S4Vectors', 'IRanges'

VignetteBuilder 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', 'knitr', 'matrixStats', 'mnormt', 'pgdraw', 'reshape2',
  'Rcpp', 'RcppProgress', 'coda', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RSQLite', 'DBI', 'dimRed', 'loe'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'crosstalk', 'rmarkdown', 'formatR', 'tibble', 'testthat',
  'styler', 'lintr', '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:
  'ggplot2', 'gridExtra', 'plyr', 'scales'

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:
  'here', 'stringr', 'readxl', 'magrittr', 'readr', 'purrr', 'ggplot2',
  'glue', 'dplyr', 'librarian', 'openxlsx', 'knitr', 'beepr',
  'tidytext', 'scales', 'rmarkdown', 'textclean', 'sf', 'tgamtheme',
  'crayon'

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:
  'assertthat', 'data.table', 'futile.logger', 'httr', 'jsonlite',
  'purrr', 'stringr', 'uuid'

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: 'rjson', 'RCurl', 'plyr'

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:
  'sampleSelection', 'maxLik', 'mfx', 'mlogit', 'mvProbit', 'knitr',
  'stargazer'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/ExtendedAppendix.Rnw'
   'inst/doc/Manuscript.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/ExtendedAppendix.Rnw'
   'vignettes/Manuscript.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'cli', 'curl', 'xml2'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'stringr', 'lubridate', 'assertthat', 'shiny',
  'clipr', 'miniUI', 'cli'

Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'testthat', 'rmarkdown', 'httpuv', 'stringi',
  'covr', 'lintr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'triebeard'

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: 'rgdal', 'png', 'jpeg'

Packages suggested but not available for checking:
  'proj4', 'sf', 'raster', 'ncdf4', 'locfit', 'knitr', 'rmarkdown',
  'sp', 'fasterize', 'IRdisplay', 'caTools', 'shiny', 'rgeos', 'webp',
  'htmlwidgets', 'htmltools', 'leaflet', 'leafem', 'leafpop',
  'RColorBrewer', 'ragg', 'widgetframe', 'geojsonsf',
  'leaflet.providers', 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'sf', 'testthat', 'USAboundariesData', 'covr', 'knitr', 'rmarkdown',
  'dplyr', 'leaflet'

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: 'tibble'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sp'

Packages suggested but not available for checking:
  'USA.state.boundaries.data', 'install.load', 'drat', 'rgdal',
  'raster', 'ggspatial', 'ggplot2', 'knitr', 'rmarkdown', 'gotop'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rgdal'

Package suggested but not available for checking: 'diseasemapping'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maptools', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maptools', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maptools', 'sp'

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

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: 'httr', 'jsonlite', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'readr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'dplyr', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'maps', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sp', 'raster'

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble', 'tidyr'
'LazyData' is specified without a 'data' directory
Running examples in 'usedist-Ex.R' failed
The error most likely occurred in:

> ### Name: pivot_to_numeric_matrix
> ### Title: Convert a data frame in long format to a numeric matrix
> ### Aliases: pivot_to_numeric_matrix
> 
> ### ** Examples
> 
> longdata <- data.frame(
+   SampleID = paste0("Sample", c(1, 1, 1, 2, 2, 3, 3)),
+   FeatureID = paste0("Feature", c(1, 2, 3, 1, 2, 2, 3)),
+   Value = c(132, 41, 7, 56, 11, 929, 83))
> longdata
  SampleID FeatureID Value
1  Sample1  Feature1   132
2  Sample1  Feature2    41
3  Sample1  Feature3     7
4  Sample2  Feature1    56
5  Sample2  Feature2    11
6  Sample3  Feature2   929
7  Sample3  Feature3    83
> pivot_to_numeric_matrix(longdata, SampleID, FeatureID, Value)
Error: Packages "dplyr", "tidyr", "tibble" are not installed, but are needed by "usedist::pivot_to_numeric_matrix".  Please install the missing packages to use this function.
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:
  'ggplot2', 'plyr', 'dplyr', 'magrittr', 'purrr', 'scales',
  'assertthat'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'clipr', 'dplyr', 'purrr', 'recipes', 'rlang', 'tidyr', 'tune'

Packages suggested but not available for checking:
  'covr', 'modeldata', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'microservices', 'purrr', 'usethis', '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:
  'cli', 'clipr', 'crayon', 'curl', 'desc', 'fs', 'gert', 'gh', 'glue',
  'jsonlite', 'lifecycle', 'purrr', 'rappdirs', 'rlang', 'rprojroot',
  'rstudioapi', 'whisker', 'withr', 'yaml'

Packages suggested but not available for checking:
  'covr', 'knitr', 'magick', 'mockr', 'pkgload', 'rmarkdown',
  'roxygen2', 'spelling', 'styler', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: '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.
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: 'tsibble'

Packages suggested but not available for checking:
  'knitr', 'lubridate', 'rmarkdown', 'devtools', 'plotly', 'remotes',
  'tidyr', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'GGally', '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: 'HistData', 'Hmisc'

Packages suggested but not available for checking:
  'zoo', 'ggplot2', 'vcd', 'lubridate', 'aplpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tmvtnorm', 'mvtnorm', 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nlsr'

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/usl.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'usmapdata'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'ggrepel', 'knitr', 'maptools', 'proto', 'rgdal',
  'rmarkdown', 'scales', 'sp', 'stringr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tibble'
Package unavailable to check Rd xrefs: 'tibble'
Note: found 33 marked UTF-8 strings
Package required but not available: 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'plyr'

Package suggested but not available for checking: 'xts'

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:
  'cli', 'covr', 'knitr', 'rlang', 'rmarkdown', 'testthat', 'withr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'
Packages required but not available:
  'dplyr', 'purrr', 'rlang', 'tidyselect', 'utile.tools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lubridate', 'purrr', 'vctrs'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'gridExtra', 'purrr'

Package suggested but not available for checking: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'ggdag', 'gmp', 'gridExtra', 'matrixStats'
Running examples in 'utilities-Ex.R' failed
The error most likely occurred in:

> ### Name: PFD
> ### Title: Prime Factor Decomposition (PFD)
> ### Aliases: PFD print.prime.factor.decomposition
> 
> ### ** Examples
> 
> PFD(1:10)
Loading required namespace: gmp
Failed with error:  'there is no package called 'gmp''
Error in PFD(1:10) : PFD() depends on the `gmp` package.
Calls: PFD -> stopifnot
Execution halted
Packages required but not available:
  'Rcpp', 'bindata', 'mvtnorm', 'Phase123', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spatstat.geom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'stringr', 'stringdist', 'RCurl', 'dplyr'

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: 'mldr', 'ROCR'

Packages suggested but not available for checking:
  'C50', 'e1071', 'infotheo', 'kknn', 'knitr', 'randomForest',
  'rmarkdown', 'markdown', 'testthat', '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:
  'doParallel', 'data.table', 'readr', 'stringr', 'biomaRt', 'vcfR',
  'Biostrings', 'dplyr', 'tidyr', 'keras', 'AnnotationHub',
  'ensembldb', 'AnnotationFilter', 'BiocGenerics', 'GenomicFeatures',
  'GenomicRanges', 'IRanges', 'foreach', 'rtracklayer', 'xml2'

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: 'gtools'

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.
Packages required but not available:
  'DescTools', 'RColorBrewer', 'gmodels', 'haven', 'psych', 'ggplot2',
  'tibble', 'tidyr', 'dplyr', 'magrittr', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'FNN', 'RSpectra', 'RcppAnnoy', 'irlba', 'RcppProgress',
  'dqrng'

Packages suggested but not available for checking:
  'testthat', 'covr', 'bigstatsr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'jsonlite', 'curl'

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', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'knitr', 'tidyr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tm'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'vaersvax', 'vaers', 'vaersND', 'data.table', 'dplyr', 'rpivotTable'
Running examples in 'vaersNDvax-Ex.R' failed
The error most likely occurred in:

> ### Name: vaersNDvax
> ### Title: Non-Domestic Vaccine Adverse Event Reporting System (VAERS)
> ###   vaccine data for Present
> ### Aliases: vaersNDvax vaersNDvax-package
> 
> ### ** Examples
> 
> library(data.table)
Error in library(data.table) : there is no package called 'data.table'
Execution halted
Packages suggested but not available for checking:
  'vaersNDvax', 'vaers', 'vaersND', 'dplyr', 'data.table',
  'pivottabler', 'knitr', 'rmarkdown'
Running examples in 'vaersvax-Ex.R' failed
The error most likely occurred in:

> ### Name: vaersvax
> ### Title: US Vaccine Adverse Event Reporting System (VAERS) vaccine data
> ###   for Present
> ### Aliases: vaersvax vaersvax-package
> 
> ### ** Examples
> 
> library("data.table")
Error in library("data.table") : there is no package called 'data.table'
Execution halted
Packages required but not available:
  'jsonlite', 'httr', 'stringr', 'dplyr', 'purrr', 'magrittr'

Packages suggested but not available for checking: 'ggplot2', 'knitr', 'tm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gamm4', 'mvtnorm', 'truncnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lazyeval'

Packages suggested but not available for checking:
  'magrittr', 'testthat', 'stringr', '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: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenomicAlignments', 'GenomicRanges', 'IRanges', 'Rsamtools', 'plyr',
  'ggplot2', 'pheatmap', 'ggplotify', 'ggpubr', '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:
  'httr', 'purrr', 'jsonlite', 'dplyr', 'magrittr', 'tibble', 'tidyr',
  'sf', 'leaflet', 'ggplot2', 'htmltools', 'stringr', 'ggspatial',
  'geojsonio', 'rlang', 'Cairo'

Packages suggested but not available 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: 'moments'

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:
  'dplyr', 'stringr', 'janitor', 'rlang', 'tidyselect', 'purrr',
  'magrittr', 'tidyr', 'tibble', 'gtools', 'listviewer', 'data.table',
  'scales', 'BBmisc', 'framecleaner', 'badger', 'rlist'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testit', '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: 'validate', 'dplyr', 'dbplyr'

Packages suggested but not available for checking:
  'testthat', 'RSQLite', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'settings', 'yaml'

Packages suggested but not available for checking:
  'rsdmx', 'tinytest', 'knitr', 'bookdown', 'lumberjack', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'truncnorm', 'triangle', 'reshape2', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'validate', 'lpSolveAPI'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'Rcpp', 'readr', 'rlang', 'rtracklayer',
  'stringr', 'tibble'

Packages suggested but not available for checking:
  'bench', 'covr', 'cowplot', 'curl', 'DBI', 'dbplyr', 'devtools',
  'DT', 'GenomicRanges', 'IRanges', 'knitr', 'purrr', 'RMariaDB',
  'rmarkdown', 'S4Vectors', '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: 'cowplot', 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'capushe', 'roxygen2'

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', '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:
  'sf', 'leaflet', 'htmltools', 'dplyr', 'devtools', 'h3jsr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rdpack'

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:
  'psych', 'EFA.MRFA', 'GPArotation', 'PCovR', 'moments', 'corpcor',
  'lavaan', 'fungible', 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Seurat', 'SeuratObject', 'sctransform'
Packages required but not available:
  'dplyr', 'httr', 'rlang', 'urltools', 'readr', 'digest', 'sf',
  'tibble', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'lwgeom', '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: 'ROCR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bio3d', 'cowplot', 'fastcluster', 'ggplot2', 'openxlsx', 'reshape2',
  'scales'

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:
  'gdata', 'dplyr', 'ggplot2', 'rlang', 'tidyverse', 'car', 'purrr',
  'formula.tools', 'gplots', 'rstatix', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'changepoint', 'e1071', 'ggplot2', 'VGAM'

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', 'markdown', '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: '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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'R6', 'glue', 'tibble', 'magrittr', 'dplyr', 'stringr', 'crayon'

Packages suggested but not available for checking:
  'testthat', 'purrr', 'knitr', 'rmarkdown', '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: 'latticeExtra', 'Rcpp', 'nor1mix'

Packages suggested but not available for checking:
  'curl', 'glmnet', 'qtl', '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:
  'RcppEigen', 'foreach', 'doParallel', 'doRNG', 'pesel'

Packages suggested but not available for checking:
  '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:
  'MTS', 'igraph', 'pracma', 'mvtnorm', 'sparsevar', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'data.table', 'stringr', 'surveyplanning', 'laeken'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SAM', 'caret', 'lm.beta', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'XML', 'XML2R', 'curl', 'stringr', 'stringi', 'RISmed'

Packages suggested but not available 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: 'gee', 'expm', 'energy'

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:
  'rstan', 'ggplot2', 'Formula', 'gridExtra'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'measures', 'party'

Packages suggested but not available for checking: 'testthat', 'ranger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gstat', 'sp', 'testthat'

Package suggested but not available for checking: 'geoR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'dplyr', 'yaml', 'openxlsx', 'VennDiagram', 'assertthat',
  'magrittr', 'tidyr', 'doParallel', 'foreach'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'futile.logger'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jmcm', 'expm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'pracma', 'rgl', 'deldir', 'zoo', 'sf', 'gstat', 'Metrics',
  'hydroGOF', 'tictoc'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgdal', 'RFmerge'

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
Package required but not available: 'sn'

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:
  'adehabitatHS', 'kulife', 'car', 'ade4', 'IDPmisc', 'REdaS', 'ca',
  'ltm', 'psych', 'usdm'
Packages unavailable to check Rd xrefs: 'car', 'adehabitatHS', 'IDPmisc', 'kulife', 'ade4', 'ca', 'usdm', 'psych', 'REdaS', 'candisc'
Running examples in 'VARSEDIG-Ex.R' failed
The error most likely occurred in:

> ### Name: VARSEDIG
> ### Title: Variable selection to discriminate among taxonomic groups
> ### Aliases: VARSEDIG
> ### Keywords: VARSEDIG
> 
> ### ** Examples
> 
> 
> data(characiformes)
> 
> VARSEDIG(data = characiformes , variables = c("M2","M3","M4","M5","M6","M7","M8","M9","M10",
+ "M11","M12","M13","M14","M15","M16","M17","M18","M19","M20","M21","M22","M23",
+ "M24","M25","M26","M27","M28"), group="Species" , group1= "Moenkhausia oligolepis",
+ group2="Moenkhausia dichroura", LEGENDd=c("x='topright'", "legend = dati",
+ "col = COLORB", "lty=lty", "bty='n'", "cex=1.2", "text.font= 3"),
+ LEGENDs=c("x='topright'", "legend=unique(datosF[,'Group'])", "col = color1",
+ "pch = pcht", "bty='n'", "cex=1.2", "text.font=3"), LEGENDr=c("x='topright'",
+ "legend = dati", "col=col", "pch= c(16,16)", "bty='n'", "cex=1.2", "text.font=3"),
+ XLIMs=c(-1.2,1.2), YLIMs=c(-1.3,1.3), BIVTEST12=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), BIVTEST21=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), colbiv="blue", ellipse=TRUE, convex=FALSE)
Error in loadNamespace(x) : there is no package called 'kulife'
Calls: VARSEDIG ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'Rcpp', 'ggplot2', 'shiny', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'htmltools', 'scales', 'plyr'

VignetteBuilder 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:
  'dplyr', 'magrittr', 'purrr', 'tidyr', 'stringr', 'glue', 'DT',
  'rstudioapi', 'rio'

Packages suggested but not available 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:
  'vars', 'ars', 'corpcor', 'strucchange', 'mvtnorm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rticles', '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: 'HI', 'minqa', 'mvnfast'

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:
  'strucchange', 'urca', 'lmtest', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Packages required but not available:
  'mvtnorm', 'alabama', 'merDeriv', 'anocva', 'corpcor', 'quadprog',
  'lme4', 'nlmeU', 'purrr', 'saemix', 'msm', 'foreach', 'doParallel'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'EnvStats'

VignetteBuilder 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', 'sn', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spam', 'glmnet', 'lhs', 'mlr', 'mlrMBO', 'RandomFields',
  'optimParallel', 'ParamHelpers', 'pbapply', 'smoof', 'sp'

Packages suggested but not available for checking:
  'DiceKriging', 'gstat', 'knitr', 'microbenchmark', 'rmarkdown',
  'R.rsp', 'spData'

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: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'gamlss', 'gamlss.dist', '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: 'R6', 'getPass', 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'mockery', 'processx', 'rmarkdown', 'testthat', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
Packages required but not available: 'ergm', 'network', 'mclust', 'sna'

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.
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Package required but not available: 'tensorA'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'copula', 'VineCopula'

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: 'lme4', 'numDeriv'

Packages suggested but not available for checking:
  'VFP', 'STB', 'knitr', 'rmarkdown', 'prettydoc'

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: 'VineCopula', 'mosum', '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: 'vcd', 'gnm', 'ca'

Packages suggested but not available for checking:
  'gmodels', 'Fahrmeir', 'effects', 'VGAM', 'plyr', 'lmtest',
  'ggplot2', 'Sleuth2', 'car', 'rgl', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'colorspace', 'lmtest'

Packages suggested but not available for checking:
  'mvtnorm', 'kernlab', 'HSAUR3', 'coin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'dplyr', 'magrittr', 'memuse', 'pinfsc50', 'Rcpp', 'stringr',
  'tibble', 'vegan', 'viridisLite'

Packages suggested but not available for checking:
  'adegenet', 'ggplot2', 'knitr', 'poppr', 'reshape2', 'rmarkdown',
  'scales', '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: 'mathjaxr', 'Rdpack', '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: 'knitr', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partykit', 'formula.tools', 'numDeriv', 'ucminf', 'zoo', 'sandwich',
  'strucchange'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'httr', 'webmockr', 'urltools', 'yaml', 'R6', 'base64enc',
  'rprojroot', 'cpp11'

Packages suggested but not available for checking:
  'roxygen2', 'jsonlite', 'testthat', 'knitr', 'rmarkdown', 'desc',
  'crayon', 'cli', 'curl', '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: 'ellipsis', 'glue', 'rlang'

Packages suggested but not available for checking:
  'bit64', 'covr', 'crayon', 'dplyr', 'generics', 'knitr', 'pillar',
  'pkgdown', 'rmarkdown', 'testthat', 'tibble', 'withr', 'xml2',
  'waldo', 'zeallot'

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', 'geomorph', 'scatterplot3d'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'stringr', 'drc', 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'compositions'

Packages suggested but not available for checking:
  'ggplot2', 'ggthemes', 'ggtern'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'quantreg', 'proxy', 'gridExtra'

Packages suggested but not available for checking:
  'rsm', 'Vdgraph', 'AlgDesign', 'knitr', 'lhs'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/vdg.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'permute', 'AlgDesign'

Package suggested but not available for checking: 'akima'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'diffobj', 'glue', 'htmltools', 'lifecycle', 'rlang', 'testthat',
  'xml2', 'cpp11'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'roxygen2', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'stringdist'

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: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'ggplot2', 'plyr', 'dplyr', 'viridis', 'gridExtra', 'knitr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'corrplot', 'gtools', 'pander', 'purrr', 'reshape2', 'qgraph',
  'VennDiagram'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'misc3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'biwavelet', 'iterators', 'spam', 'maps', 'fields', 'foreach', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'htmlwidgets', 'htmltools', 'magrittr', 'digest',
  'clipr', 'webshot', 'base64'

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: 'vegan', 'rgl', 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'permute'

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:
  'jsonlite', 'htmlwidgets', 'assertthat', 'rlang', 'glue', 'magrittr',
  'htmltools', 'digest'

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'listviewer', 'testthat', 'yaml',
  'fs', 'usethis', 'readr', 'tibble', 'lubridate', 'V8', 'withr',
  'learnr', 'rsvg', 'dplyr', 'png', 'conflicted', 'here', 'shiny',
  'purrr', 'rsconnect'

VignetteBuilder 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', 'vegan'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'RColorBrewer', 'smacof'

VignetteBuilder 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', 'RCurl', 'DBI', 'RSQLite', 'dplyr', 'rlang', 'readr',
  'dbplyr', 'magrittr', 'hoardr', 'xml2', 'httr', 'plyr', 'tibble'

Packages suggested but not available for checking:
  'vegan', 'labdsv', 'akima', 'googleVis', 'indicspecies', 'uuid',
  'knitr', 'stringr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/vegdata.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'curl', 'tinytest'
Packages required but not available:
  'taxlist', 'knitr', 'qdapRegex', 'sp', 'stringi', 'vegdata'

Packages suggested but not available for checking:
  'rmarkdown', 'roxygen2', 'testthat', 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'data.table', 'units', 'dotCall64', 'cptcity', 'fields'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'lwgeom'

VignetteBuilder 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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'httr', 'stringr', 'magrittr', 'glue', 'assertthat',
  'lifecycle'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'here', 'fs', 'conflicted',
  'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'futile.logger'

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:
  'Rcpp', 'foreach', 'VennDiagram', 'visNetwork', 'igraph',
  'RcppEigen', 'RcppNumerical'

Packages suggested but not available 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', 'stringr', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'admisc'

Packages suggested but not available for checking:
  'QCA', 'ggplot2', 'ggpolypath'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pedtools', 'ribd'

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', 'dplyr'
'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: 'fields', 'CircStats', 'dtw'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat'
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
'LazyData' is specified without a 'data' directory
Package required but not available: 'numbers'

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', 'snowfall'

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: 'oro.nifti', 'pbmcapply', 'pbapply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'butcher', 'cli', 'curl', 'generics', 'glue', 'hardhat', 'httr',
  'jsonlite', 'lifecycle', 'pins', 'plumber', 'purrr', 'rapidoc',
  'readr', 'renv', 'rlang', 'tibble', 'vctrs', 'withr'

Packages suggested but not available for checking:
  'caret', 'covr', 'knitr', 'LiblineaR', 'mlr3', 'mlr3learners',
  'modeldata', 'parsnip', 'ranger', 'recipes', 'rmarkdown',
  'rsconnect', 'testthat', 'workflows', '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:
  'sp', 'stringr', 'tis', 'lubridate', 'maptools', 'plyr', 'xts',
  'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'lme4', 'lmerTest', 'multcomp'

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'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'copula', 'extraDistr', 'stringr'

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:
  'shiny', 'htmltools', 'jsonlite', 'scales'

Packages suggested but not available for checking:
  'RColorBrewer', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gnm', 'VCA'

Packages suggested but not available for checking:
  'RUnit', 'knitr', 'rmarkdown', 'prettydoc'

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: 'e1071', 'nleqslv'

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: 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'VGAM'

Package suggested but not available for checking: 'VGAMdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'VGAMextra'

Package which this enhances but not available for checking: 'VGAMdata'
Packages unavailable to check Rd xrefs: 'VGAMdata', 'VGAMextra', 'car'
Packages required but not available:
  'Biostrings', 'coRdon', 'ggplot2', 'seqinr', 'stringr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'e1071'

Packages suggested but not available for checking: 'pamr', 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ape', 'plotrix', 'seqinr', 'gtools'
Running examples in 'vhica-Ex.R' failed
The error most likely occurred in:

> ### Name: CUB
> ### Title: Computes the Codon Usage Bias of DNA sequences
> ### Aliases: CUB
> 
> ### ** Examples
> 
> 	seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
> 	CUB(seq.file)
Error in CUB(seq.file) : Reading FASTA files require package seqinr
Execution halted
Packages required but not available:
  'utf8', 'crul', 'jsonlite', 'assertthat', 'magrittr', 'stringr',
  'tibble', 'tidyr', 'purrr', 'dplyr', 'rlang'

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:
  'lubridate', 'Rcpp', 'foreach', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'ggplot2', 'Rdpack', 'rjags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'DT', 'ggplot2', 'ggpubr', 'shiny', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'httr', 'sf', 'dplyr', 'purrr', 'cli', 'DBI', 'xml2',
  'glue', 'dbplyr', 'rlang', 'curl', 'rvest', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'leaflet'

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'
Note: found 60 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: 'gsubfn', 'sf', 'utf8'

Packages suggested but not available for checking:
  'testthat', 'R.rsp', 'DT'

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', 'rstudioapi', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'shinythemes', 'shinyWidgets', 'shinydashboard',
  'config', 'golem', 'JBrowseR', 'dplyr', 'tidyr', 'DT', 'ggplot2',
  'ggpubr', 'plotly', 'vroom', 'abind', 'reshape2', 'markdown', 'rlang'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
vif: no visible global function definition for 'sd'
vif: no visible global function definition for 'lm'
vif: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Packages required but not available:
  'PCAmixdata', 'ggplot2', 'Polychrome', 'mclust', 'rlang'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SuperLearner', 'dplyr', 'magrittr', 'ROCR', 'tibble', 'rlang',
  'data.table'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gam', 'xgboost', 'glmnet', 'ranger',
  'polspline', 'quadprog', 'covr', 'testthat', 'ggplot2', 'cowplot',
  'cvAUC', '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:
  'colorspace', 'car', 'magrittr', 'robustbase', 'sp', 'vcd', 'e1071',
  'Rcpp', 'laeken', 'ranger', 'data.table'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'knitr', 'rmarkdown', 'reactable'

VignetteBuilder 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: 'purrr', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'ADGofTest'

Packages suggested but not available for checking:
  'TSP', 'shiny', 'testthat', 'numDeriv', 'kdecopula', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvinecopulib', 'kde1d', 'Rcpp', 'assertthat', 'RcppEigen', 'BH',
  'wdm', 'RcppThread'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'AppliedPredictiveModeling',
  'quantreg', 'tidyr', 'dplyr', 'purrr', 'scales', '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:
  'copula', 'ADGofTest', 'cubature', 'TSP'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sm', 'zoo'

Packages suggested but not available for checking:
  'ggplot2', 'RColorBrewer', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'beeswarm', 'ggplot2', 'beanplot', 'vioplot',
  'ggbeeswarm'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'methodComparison.Rnw' using Sweave

Error: processing vignette 'methodComparison.Rnw' failed with diagnostics:
 chunk 2 (label = simData) 
Error in library(beeswarm) : there is no package called 'beeswarm'

--- failed re-building 'methodComparison.Rnw'

--- re-building 'usageExamples.Rnw' using Sweave

Error: processing vignette 'usageExamples.Rnw' failed with diagnostics:
 chunk 18 (label = showGg) 
Error in library(ggbeeswarm) : there is no package called 'ggbeeswarm'

--- failed re-building 'usageExamples.Rnw'

SUMMARY: processing the following files failed:
  'methodComparison.Rnw' 'usageExamples.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'gridExtra', 'magrittr', 'plyr', 'tibble'

Packages suggested but not available for checking:
  'DT', 'C50', 'caret', 'Ckmeans.1d.dp', 'covr', 'Cubist',
  'doParallel', 'dplyr', 'earth', 'fastshap', 'gbm', 'glmnet', 'h2o',
  'htmlwidgets', 'keras', 'knitr', 'mlbench', 'mlr', 'mlr3',
  'neuralnet', 'NeuralNetTools', 'parsnip', 'party', 'partykit', 'pdp',
  'pls', 'randomForest', 'ranger', 'rmarkdown', 'RSNNS', 'sparkline',
  'sparklyr', 'tinytest', 'varImp', '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:
  'rmgarch', 'mgarchBEKK', 'gnm', 'expm', 'BigVAR', 'ks', 'matrixcalc',
  'matlib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'hexbin', 'ggplot2', 'testthat', 'covr'
Running examples in 'viridisLite-Ex.R' failed
The error most likely occurred in:

> ### Name: viridis
> ### Title: Viridis Color Palettes
> ### Aliases: viridis viridisMap magma inferno plasma cividis rocket mako
> ###   turbo
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'viridisLite', 'ggplot2', 'gridExtra'

Packages suggested but not available for checking:
  'hexbin', 'scales', 'knitr', 'dichromat', 'colorspace', 'raster',
  'rasterVis', 'httr', 'mapproj', 'vdiffr', 'svglite', 'testthat',
  'covr', 'rmarkdown', 'rgdal', 'maps'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'viridis', 'plyr', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'formatR', 'kableExtra', '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: 'raster', 'ade4', 'rworldmap', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'odbc', 'processx', 'DBI', 'ini', 'rappdirs', 'curl', 'fs', 'digest',
  'ps'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'nycflights13', 'testthat', 'covr', 'jsonld',
  'dplyr', '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', 'plyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'lintr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'htmlwidgets'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown', 'tibble', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'dplyr', 'ggplot2', 'magrittr', 'shinyjs', 'ca', 'tidyr',
  'ggrepel', 'rlang', 'DT'

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:
  'ggplot2', 'ggpmisc', 'reshape2', 'RColorBrewer'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'flux', 'knitr', 'rmarkdown', '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:
  'doParallel', 'foreach', 'scales', 'plotrix', 'Rdpack', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Cairo', 'testthat', 'pracma', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'dplyr', 'purrr', 'readr', 'magrittr', 'tibble',
  'glue'

Packages suggested but not available for checking:
  'testthat', 'plotly', 'knitr', 'rmarkdown', 'vdiffr', 'gdtools',
  '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:
  'chron', 'colorspace', 'stringr', 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rssa', 'ggplot2', 'ggthemes', '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:
  'rstan', 'Rcpp', 'sqldf', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'knitr', 'shiny', 'rmarkdown', 'pander', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'htmltools', 'jsonlite', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'webshot', 'igraph', 'shiny', 'shinyWidgets',
  'colourpicker', 'sparkline', 'ggraph', 'tidygraph', 'flashClust'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rgl', 'knitr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'broom', 'DT', 'magrittr', 'ggplot2', 'tidyr', 'dplyr', 'kableExtra',
  'gt', 'tidyselect', 'parcats', 'cowplot', 'gtable', 'gridExtra',
  'rlang'

Packages suggested but not available for checking:
  'covr', 'testthat', 'vdiffr', 'knitr', 'rmarkdown', 'forcats',
  'glue', 'tibble', '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:
  'vcd', 'Cairo', 'multcompView', 'nortest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'assertive.types', 'plotly', 'ggplot2', 'ggrepel',
  'RColorBrewer'

Packages suggested but not available for checking:
  'prettydoc', 'knitr', 'testthat', 'covr', 'highcharter'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'partykit', 'colorspace'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'magrittr'

Packages suggested but not available for checking:
  'covr', '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.
Packages required but not available:
  'Hmisc', 'dplyr', 'polyclip', 'deldir', 'plotrix', 'gtools',
  'combinat', 'XML', 'oro.dicom', 'rlang', 'shiny', 'shinyjs', 'DT',
  'htmlTable', 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cranlogs', 'plotly', 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', 'devtools', 'roxygen2', '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:
  'gbm', 'randomForest', 'e1071', 'magrittr', 'FactoMineR', 'ggplot2',
  'mltools', 'dplyr', 'data.table', 'MBA', 'pROC', 'ggrepel'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'egg'

VignetteBuilder 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', 'splitstackshape', 'tidyr', 'PBSmapping',
  'formattable', 'ggplot2', 'plot3D', 'ggdendro', 'ggrepel', 'readxl',
  'WriteXLS', 'DT', 'psych', 'pracma', 'Rtsne', 'plyr', 'svglite',
  'Cairo', 'tikzDevice', 'shinybusy', 'Rdpack'

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', 'shinyhelper', 'shinycssloaders', 'bsplus', 'DT', 'ggplot2',
  'dplyr', 'readr', 'tidyr', 'fastcluster', 'clusterCrit', 'dunn.test',
  'RColorBrewer', 'dendextend', 'ComplexHeatmap', 'circlize',
  'patchwork', 'knitr', 'kableExtra'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'glue', 'dplyr', 'rmarkdown', 'knitr', 'xfun', 'yaml',
  'tibble', 'vctrs', 'pillar', 'jsonlite'

Packages suggested but not available for checking:
  'covr', 'rorcid', 'testthat', 'stringr', 'htmltools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'randomForest'

Package suggested but not available for checking: 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'condvis2', 'ggplot2', 'GGally', 'RColorBrewer', 'colorspace',
  'DendSer', 'ggalt', 'dplyr', 'igraph', 'flashlight', 'ggnewscale',
  'tidyr'

Packages suggested but not available for checking:
  'intergraph', 'network', 'sna', 'mlr', 'tidymodels', 'e1071',
  'gridExtra', 'lemon', 'mlr3', 'mlr3learners', 'sp', 'scales',
  'ranger', 'vip', 'knitr', 'rmarkdown', 'randomForest', 'testthat',
  'labeling', 'zenplots', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'DALEX'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mlbench', 'randomForest', 'gridExtra',
  'testthat', 'ingredients'

VignetteBuilder 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', 'htmlwidgets', 'magrittr', '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: 'httr', 'purrr', 'jsonlite', 'XML'

Packages suggested but not available for checking:
  'stringr', 'tm', 'plyr', 'dplyr', 'reshape2', 'jpeg', 'igraph',
  'rgexf', 'httpuv', 'mongolite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'checkmate', 'magrittr', 'dplyr', 'tidyr', 'BH',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'spcadjust', 'testthat', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggrepel', 'ggplot2', 'ggiraph', 'ggsci'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines")
to your NAMESPACE file.
Packages required but not available:
  'dtw', 'tseries', 'RTransferEntropy', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'magrittr', 'reshape2', 'scales', 'R6'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'nnfor', 'vmd'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'readr', 'stringr', 'tidyr', 'purrr', 'ggpubr', 'imager',
  'av', 'dplyr', 'rlang', 'foreach', 'magrittr', 'pracma', 'crayon',
  'svDialogs', 'pdftools', 'doFuture', 'progressr', 'future', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jsonlite', 'curl'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ssh'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'trust'

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: 'igraph'
Packages required but not available:
  'plotly', 'ggplot2', 'ggpubr', 'ggrepel'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', '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: 'Rcpp', 'RcppEigen', 'BH'

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:
  'dplyr', 'tidyr', 'knitr', 'rmarkdown', 'ggplot2', 'diverse',
  'geosphere', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 4954 marked UTF-8 strings
Packages required but not available:
  'dplyr', 'dismo', 'fields', 'ggplot2', 'ggtext', 'latticeExtra',
  'raster', 'rangeBuilder', 'rgeos', 'terra', 'viridisLite', 'sp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'covr', 'gridExtra', 'rgdal', 'rmarkdown',
  'rnaturalearth', 'rnaturalearthdata', '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:
  'data.tree', 'rlang', 'htmlwidgets', 'shiny', 'shinyjs', 'DT'

Packages suggested but not available for checking:
  'rmarkdown', 'scales', '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:
  'betareg', 'data.table', 'ggplot2', 'glmulti', 'gtools', 'GGally',
  'irr', 'plyr', 'R.utils', 'stringr', 'vortexRdata'

Packages suggested but not available for checking:
  'devtools', 'gridExtra', '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:
  'data.table', 'httpuv', 'httr', 'igraph', 'magrittr', 'RColorBrewer',
  'shiny', 'SnowballC', 'systemfonts', 'syuzhet', 'textutils', 'tm',
  'vosonSML', 'wordcloud'

Packages suggested but not available for checking:
  'dplyr', 'DT', 'htmlwidgets', 'rtweet', 'shinydashboard', 'shinyjs',
  'visNetwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'Hmisc', 'httpuv', 'httr', 'igraph',
  'jsonlite', 'lubridate', 'magrittr', 'purrr', 'RCurl', 'rlang',
  'rtweet', 'stringr', 'textutils', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'stopwords', 'testthat', 'tictoc', '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', 'httr', 'jsonlite', 'magrittr', 'openssl', 'rlang',
  'stringr', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'scales', '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:
  'formattable', 'knitr', 'data.table', 'fields'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gestalt', 'glue', 'httr', 'jsonlite', 'lubridate',
  'magrittr', 'purrr', 'snakecase', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'conflicted', 'covr', 'knitr', 'rmarkdown', 'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'gtools'

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: 'shiny', 'glue', 'htmltools'

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:
  'fda', 'gamm4', 'RLRsim', 'oro.nifti', 'shape', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lmerTest', 'gamm4', 'oro.nifti', 'ggplot2', 'purrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'FNN', 'Rfast', 'circular', 'dplyr', 'fastcluster',
  'geometry', 'raster', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'classInt', 'dplyr', 'ggplot2', 'readr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'knitr', 'testit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'oce', 'dplyr', 'interp', 'magick', 'gsw', 'tidyr',
  'stringr', 'metR', 'gridExtra', 'lubridate', 'usethis'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'akima', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'misc3d'
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in 'vrmlgen-Ex.R' failed
The error most likely occurred in:

> ### Name: cloud3d
> ### Title: Draw a 3D scatter plot
> ### Aliases: cloud3d
> ### Keywords: utilities misc
> 
> ### ** Examples
> 
> 
> 
> curdir <- getwd()
> outdir <- tempdir()
> setwd(outdir)
> 
> 
> # example 1: visualize random 3D input data
> mat <- matrix(runif(99, 0, 3), ncol = 3)
> 
> # create random class assignment vector with three classes
> y <- round(runif(33, 0, 2))
> y <- ifelse(y == 0, "class 1", ifelse(y == 1, "class 2", "class 3"))
> 
> # create ouput using numbers from 1 to length(y) as metalabels
> cloud3d(mat, labels = y, metalabels = 1:length(y), col.axis = "black",
+         col.lab = "blue", col.bg = "white", type = "vrml",
+         filename = "result.wrl", htmlout = "result.html")

Output file "result.wrl" was generated in folder C:/r_packages/pkgcheck/CRAN/vrmlgen/tmp/Rtmpodfp3k.
> 
> # show the output in a web-browser 
> # (VRML-plugin must be installed!)
> if(file.exists(paste("file://",file.path(outdir,
+                 "result.html"), sep = "")))
+ {
+   browseURL(paste("file://",file.path(outdir,
+                   "result.html"), sep = ""))
+ }
> 
> 
> # example 2: visualization of Edgar Anderson's Iris data
> # using density estimation contour surfaces (requires misc3-package!)
> irismat <- iris[,1:3]
> cloud3d(irismat, labels = iris[,5], vrml_showdensity = TRUE,
+         col.axis = "blue", col.lab = "black", lab.axis = colnames(irismat),
+         type = "vrml", filename = "result2.wrl", htmlout = "iris.html")
Loading required package: misc3d
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'misc3d'
Error in .vdensecalc(x, h = h, weights = weights, rawdata = rawdata, filename = filename) : 
  In order to draw contour surfaces, please first install the misc3d package!
Calls: cloud3d -> .vcloud -> .vdense -> .vdensecalc
Execution halted
Packages required but not available:
  'ica', 'lpSolveAPI', 'nnls', 'quadprog'

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:
  'bit64', 'crayon', 'cli', 'glue', 'hms', 'lifecycle', 'rlang',
  'tibble', 'tzdb', 'vctrs', 'tidyselect', 'withr', 'progress', 'cpp11'

Packages suggested but not available for checking:
  'archive', 'bench', 'covr', 'curl', 'dplyr', 'forcats', 'fs',
  'ggplot2', 'knitr', 'patchwork', 'prettyunits', 'purrr', 'rmarkdown',
  'rstudioapi', 'scales', 'spelling', 'testthat', 'tidyr', 'waldo',
  'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'teigen', 'mclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Hmisc', 'ggplot2', 'reshape', 'lfe', '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', 'dplyr', 'survminer', 'flexsurv', 'magrittr', 'ggpubr',
  'muhaz'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fitdistrplus', 'Rcpp'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/vsgoftest_tutorial.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'glue', 'invertiforms', 'LRMF3', 'magrittr', 'rlang',
  'RSpectra', 'tibble', 'withr'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'GGally', 'igraph', 'igraphdata', 'knitr', 'purrr',
  'rmarkdown', 'scales', 'testthat', 'tidygraph', '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: 'R6', 'httr', 'RCurl', '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:
  'doParallel', 'foreach', 'Rborist', 'randomForest', '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:
  'kableExtra', 'rstudioapi', 'sjlabelled', 'haven', 'knitr'

Packages suggested but not available for checking: '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: 'wrapr', 'digest'

Packages suggested but not available for checking:
  'rquery', 'rqdatatable', 'data.table', 'isotone', 'lme4', 'knitr',
  'rmarkdown', 'DBI', 'RSQLite', 'R.rsp', 'tinytest'

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:
  'DiagrammeR', 'DiagrammeRsvg', 'rsvg', 'htmlwidgets', 'shiny'

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: 'shiny', 'rmarkdown', 'EnvStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'randomForest'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmltools', 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', '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: 'XML', 'plyr'

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.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'polyclip', 'gridBezier'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rlang', 'ggplot2', 'shiny', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gridExtra', 'itsadug'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'waveslim', 'wavemulcor', 'colorspace'

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', 'rvest', 'lubridate', 'magrittr', 'tibble', '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: 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'cli', 'rstudioapi', 'colorspace', 'viridis', 'knitr', 'rmarkdown',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mclust', 'mnormt', 'tmvtnorm', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xgboost', 'tokenizers', 'text2vec', 'R6', 'tibble', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'RColorBrewer', 'gridExtra', 'gtable', 'extrafont'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
summary.whc: no visible global function definition for 'printCoefmat'
wahc.fit: no visible global function definition for 'pt'
wahc.fit: no visible global function definition for 'cor'
whc: no visible global function definition for 'model.frame'
whc: no visible global function definition for 'model.matrix'
whc: no visible global function definition for 'model.response'
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
Packages required but not available: 'R6', 'shiny', 'htmltools'

Packages suggested but not available for checking:
  'httr', 'knitr', 'packer', 'rmarkdown'

VignetteBuilder 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', 'ggplot2', 'dplyr', '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:
  'cli', 'diffobj', 'fansi', 'glue', 'rematch2', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'covr', 'R6', 'testthat', 'withr', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayesplot', 'Rcpp', 'rstan', 'coda', 'dplyr', 'Hmisc', 'ggplot2',
  'KFAS', 'loo', 'RcppParallel', 'rlang', 'rstantools', 'StanHeaders',
  'BH', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
  'diagis', 'gridExtra', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'leaflet', 'shiny', 'dismo', 'dplyr', 'DT', 'ecospat', 'ENMeval',
  'jsonlite', 'leaflet.extras', 'magrittr', 'raster', 'RColorBrewer',
  'rgeos', 'rgdal', 'rmarkdown', 'shinyjs', 'sp', 'spocc', 'spThin',
  'zip'

Packages suggested but not available for checking:
  'knitr', 'rgbif', 'testthat', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'prodlim', 'riskRegression', '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:
  'glue', 'purrr', 'httr', 'tibble', 'magrittr', 'stringr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'freesurferformats', 'imager', 'jpeg', 'png', 'spacesXYZ'

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: 'WRS2', 'ggplot2', 'jmvcore', 'R6'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magrittr'

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: 'covr', 'tinytest'
Packages required but not available: 'lubridate', 'readtext', 'flextable'

Packages suggested but not available 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:
  'tuneR', 'seewave', 'NatureSounds', 'dtw', 'fftw', 'monitoR',
  'pbapply', 'RCurl', 'rjson', 'Rcpp', 'knitr', 'crayon',
  'bioacoustics', 'stringi'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'jpeg', 'ape', 'soundgen', 'wavethresh',
  'png', 'pracma', 'Sim.DiffProc', 'maps', 'leaflet', 'kableExtra'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'fda', 'fields', 'reshape2', 'lme4'

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'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'gplots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rlang', 'curl', 'httr', 'xml2', '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: 'waveslim', 'tidyr', 'ggplot2', 'sp'

Packages suggested but not available for checking:
  'zoo', 'FNN', 'readr', 'knitr', 'cowplot', 'gridGraphics',
  'bookdown', 'rmarkdown', 'SPEI', 'NPRED', 'synthesis', 'kableExtra',
  'fitdistrplus', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH', 'RcppArmadillo'

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:
  'latticeExtra', 'xml2', 'lubridate', 'dataRetrieval'

Packages suggested but not available for checking:
  'xtable', 'maps', 'mapdata'

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:
  'raster', 'rgdal', 'purrr', 'caret', 'vctrs', 'magrittr', 'dplyr',
  'pingr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'tibble', 'rmarkdown', 'covr', 'tmap',
  'tmaptools', 'OpenStreetMap', '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: 'sp', 'maptools', 'rgeos', 'splancs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'wavethresh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'lintr', '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: 'wavelets', 'fracdiff', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'wavelets', 'fracdiff', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wavelets', 'FinTS', 'forecast', 'rugarch', 'fracdiff'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wavelets', 'fracdiff', 'forecast', 'randomForest', 'tsutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wavelets', 'fracdiff', 'forecast', 'e1071', 'tsutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'waveslim', 'plot3D', 'RColorBrewer'

Packages suggested but not available for checking:
  'covr', 'knitr', 'markdown', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgdal', 'sp', 'geosphere', 'rgeos'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kimisc'

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', 'ggplot2', 'ggvoronoi', 'sampling',
  'BalancedSampling', 'sp', 'sf'

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: 'fftw', 'covr'
Packages required but not available:
  'caret', 'dplyr', 'ggplot2', 'lifecycle', 'magrittr', 'pls',
  'prospectr', 'randomForest', 'readr', 'rlang', 'scales',
  'spectacles', 'stringr', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'abind', 'colorRamps', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'deSolve', 'dplyr', 'colorRamps',
  'ggplot2', 'gridExtra', 'latticeExtra', 'bindrcpp'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'hexbin'

Packages suggested but not available for checking:
  'modi', 'robustbase', 'robustX', 'cellWise', '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: 'simpleboot'

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:
  'dplyr', 'httr', 'jsonlite', 'lifecycle', 'lubridate', 'readr',
  'rlang', 'stringr', 'tibble', 'tidyr', 'magrittr'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'wavelets', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'tidyr', 'progress', 'countrycode', 'tibble',
  'purrr', 'stringr', 'readr', 'forcats'

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown', 'tidyverse', 'lemon'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coin', 'dplyr', 'progress', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

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: 'pracma', 'raster'

Package suggested but not available for checking: 'rmarkdown'

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:
  'minqa', 'mnormt', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'captioner', 'doBy'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
onesamplemeantest: no visible global function definition for 'pnorm'
twosamplemeantest: no visible global function definition for 'pnorm'
wcq: no visible global function definition for 'var'
wcq: no visible global function definition for 'pnorm'
wcq.fdrc: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Package required but not available: 'RJSONIO'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'binman', 'assertthat', 'processx', 'yaml', 'semver'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'Hmisc', 'copula', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'arcpullr', 'sf', 'httr', 'jsonlite', 'dplyr', 'ggplot2', '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:
  'sf', 'sp', 'assertthat', 'progress', 'curl', 'httr', 'countrycode',
  'wdman', 'RSelenium', 'xml2', 'cli', 'lwgeom', 'tibble', 'rappdirs'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'roxygen2', 'rmarkdown', 'ggmap', 'ggplot2',
  'pingr', 'prepr', '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:
  'settings', 'reshape2', 'lubridate', 'magrittr', 'rlang', 'dplyr',
  'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompQuadForm', 'matrixStats', 'vars'

Packages suggested but not available for checking:
  'timeSeries', 'FitARMA', 'testthat', 'knitr', 'rmarkdown', 'renv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xts', 'lubridate', 'dplyr', 'RHRV', 'magrittr', 'signal',
  'waveslim', 'futile.logger', 'kernlab', 'padr', 'varian', 'ggplot2',
  'R.utils'

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: 'ggmap', 'lubridate', 'RJSONIO', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'xtable', 'scales', 'brew', 'fs', 'readr', 'reshape2',
  'digest'

Packages suggested but not available for checking: 'whoami', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'httr', 'rvest', 'jsonlite', 'stringr', 'dplyr', 'purrr',
  'data.tree', 'tibble', 'base64enc', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'rcdk', 'covr', 'robotstxt', 'knitr', 'rmarkdown',
  'plot.matrix', 'usethis', '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: 'httpuv', 'html5', 'stringi'

Packages suggested but not available for checking: 'dbWebForms', 'pgTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'base64enc', 'curl', 'debugme', 'httr', 'jsonlite', 'R6',
  'showimage', 'withr'

Packages suggested but not available for checking:
  'covr', 'pingr', 'rprojroot', 'servr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'knitr', 'yaml', 'rmarkdown'

Packages suggested but not available for checking:
  'testthat', 'bookdown', 'xfun'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'callr', 'curl', 'glue', 'jsonlite', 'httr', 'httpuv', 'testthat',
  'withr', 'xml2'
Packages unavailable to check Rd xrefs: 'jsonlite', 'callr', 'httr', 'glue'
Running examples in 'webfakes-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)
> url <- proc$url("/get")
Error in loadNamespace(x) : there is no package called 'callr'
Calls: <Anonymous> ... 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:
  'dplyr', 'doRNG', 'readr', 'doParallel', 'foreach', 'jsonlite',
  'httr', 'rlang', 'svglite', 'igraph', 'whisker', 'apcluster', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geojsonio', 'jsonlite', 'httpuv'

Packages suggested but not available for checking:
  'knitr', 'R.rsp', 'rmarkdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'jsonlite', 'magrittr', 'R6', 'urltools', 'fauxpas', 'crul',
  'base64enc'

Packages suggested but not available for checking:
  'testthat', 'xml2', 'vcr', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'lavaan', 'PearsonDS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'jpeg', 'png'
Running examples in 'webp-Ex.R' failed
The error most likely occurred in:

> ### Name: read_webp
> ### Title: Webp image format
> ### Aliases: read_webp webp write_webp
> 
> ### ** Examples
> 
> # Convert to webp
> library(png)
Error in library(png) : there is no package called 'png'
Execution halted
Packages required but not available: 'Rcpp', 'readr'

Packages suggested but not available for checking:
  'iptools', 'urltools', 'rgeolocate', '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:
  'moonBook', 'ggplot2', 'shiny', 'stringr', 'sjlabelled', 'flextable',
  'magrittr', 'rrtable', 'dplyr', 'tibble', 'purrr', 'rlang', 'tidyr',
  'tidyselect', 'psych', 'ztable', 'ggforce', 'scales', '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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magrittr', 'jsonlite', 'callr'

Packages suggested but not available for checking:
  'httpuv', 'knitr', 'rmarkdown', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'later', 'cpp11', 'AsioHeaders'

Packages suggested but not available for checking:
  'httpuv', '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:
  'jsonlite', 'stringr', 'crayon', 'RCurl', 'readr', 'rstudioapi',
  'pkgsearch', 'tibble', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'jsonlite', 'lubridate', 'magrittr', 'httr', 'purrr',
  'dplyr', 'readr', 'sf'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'haven'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'jsonlite'

Packages suggested but not available for checking: 'httpuv', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'DT', 'shiny', 'shinythemes'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'dplyr', 'magrittr', 'tidytext', 'stringr', 'tibble',
  'geonames', 'countrycode', 'purrr', 'tidyr', 'forcats', 'ggplot2',
  'rgeos', 'sf', 'here'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quantreg', 'doParallel', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'sp', 'raster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'furrr', 'future', 'glue', 'janitor',
  'jsonlite', 'magrittr', 'progressr', 'Rcpp', 'RcppParallel', 'rlang',
  'rvest', 'stringr', 'tidyr', 'usethis'

Packages suggested but not available for checking:
  'crayon', 'curl', 'DBI', 'ggplot2', 'ggrepel', 'httr', 'purrr',
  'rmarkdown', 'RSQLite', 'stringi', 'testthat', 'tibble', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glue', 'xtable', 'sqldf', 'R.oo', 'FAdist', 'mixdist', 'optimx',
  'kSamples', 'e1071', 'R.methodsS3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lifecycle', 'magrittr', 'plotly', 'purrr',
  'Rcpp', 'sandwich', 'segmented', 'SPREDA', 'tibble', 'tidyr',
  '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: 'TraMineR', 'RColorBrewer'

Packages suggested but not available for checking:
  'RUnit', 'knitr', 'isotone', 'vegan'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/WeightedCluster.Rnw'
   'inst/doc/WeightedClusterFR.Rnw'
   'inst/doc/WeightedClusterPreview.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GeneralisedCovarianceMeasure', 'xgboost'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'ROCR', 'pROC', 'PRROC', 'microbenchmark', 'glmnet', 'testthat',
  'ggplot2', 'GsymPoint', 'geometry'
Running examples in 'WeightedROC-Ex.R' failed
The error most likely occurred in:

> ### Name: WeightedAUC
> ### Title: WeightedAUC
> ### Aliases: WeightedAUC
> 
> ### ** Examples
> 
> 
> library(WeightedROC)
> ## Compute the AUC for this weighted data set.
> y <- c(0, 0, 1, 1, 1)
> w <- c(1, 1, 1, 4, 5)
> y.hat <- c(1, 2, 3, 1, 1)
> tp.fp <- WeightedROC(y.hat, y, w)
> (wauc <- WeightedAUC(tp.fp))
[1] 0.325
> 
> ## For the un-weighted ROCR example data set, verify that our AUC is
> ## the same as that of ROCR/pROC.
> if(require(microbenchmark) && require(ROCR) && require(pROC)){
+   data(ROCR.simple, envir=environment())
+   microbenchmark(WeightedROC={
+     tp.fp <- with(ROCR.simple, WeightedROC(predictions, labels))
+     wroc <- WeightedAUC(tp.fp)
+   }, ROCR={
+     pred <- with(ROCR.simple, prediction(predictions, labels))
+     rocr <- performance(pred, "auc")@y.values[[1]]
+   }, pROC={
+     proc <- pROC::auc(labels ~ predictions, ROCR.simple, algorithm=2)
+   }, times=10)
+   rbind(WeightedROC=wroc, ROCR=rocr, pROC=proc) #same
+ }
Loading required package: microbenchmark
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'microbenchmark'
> 
> ## For the un-weighted pROC example data set, verify that our AUC is
> ## the same as that of ROCR/pROC.
> data(aSAH, envir=environment())
Warning in data(aSAH, envir = environment()) :
  data set 'aSAH' not found
> table(aSAH$s100b)
Error in table(aSAH$s100b) : object 'aSAH' not found
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
Errors in running code in vignettes:
when running code in 'Definition.Rnw'

> y <- c(-1, -1, 1, 1, 1)

> w <- c(1, 1, 1, 4, 5)

> y.hat <- c(1, 2, 3, 1, 1)

> library(WeightedROC)

> tp.fp <- WeightedROC(y.hat, y, w)

> library(ggplot2)

  When sourcing 'Definition.R':
Error: there is no package called 'ggplot2'
Execution halted

  'Definition.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'Definition.Rnw' using Sweave

Error: processing vignette 'Definition.Rnw' failed with diagnostics:
 chunk 1 (label = curve) 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'Definition.Rnw'

SUMMARY: processing the following file failed:
  'Definition.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'mvtnorm', 'rootSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cobalt', 'ggplot2', 'crayon', 'backports'

Packages suggested but not available for checking:
  'twang', 'CBPS', 'ATE', 'optweight', 'SuperLearner', 'mlogit',
  'mclogit', 'MNP', 'brglm2', 'osqp', 'survey', 'gbm', 'dbarts',
  'knitr', 'rmarkdown'

VignetteBuilder 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', 'foreach', 'doParallel', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'scales'

Package suggested but not available for checking: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'mice', 'gdata', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'SparseM', 'xtable', 'e1071', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'SparseM', 'slam', 'e1071'
Errors in running code in vignettes:
when running code in 'wsvmdoc.Rnw'
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'wsvmdoc.Rnw'... failed to complete the test
Package required but not available: 'lme4'

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', 'wk', 'Rcpp', 'BH'

Packages suggested but not available for checking: 'leaflet', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'Rdpack'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'numDeriv', 'statmod', 'Rmpfr', 'NPflow', 'minqa'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'withr', 'tidyr', 'EdSurvey'

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:
  'ggplot2', 'mclust', 'pROC', 'reshape2', '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:
  'spray', 'mathjaxr', 'disordR', 'freealg'

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: 'arm'

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: 'dplyr', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qtl', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettydoc'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dynamicTreeCut', 'fastcluster', 'matrixStats', 'Hmisc', 'impute',
  'foreach', 'doParallel', 'preprocessCore', 'GO.db', 'AnnotationDbi',
  'Rcpp'

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'infotheo', 'entropy', 'minet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geepack', 'bindata', 'PoisNor', 'CRTgeeDR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SKAT', 'seqminer', 'data.table'

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: 'lpSolve', '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: 'colorspace', '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: 'cli', 'rstudioapi', 'jsonlite'

Packages suggested but not available for checking:
  'magrittr', 'ggplot2', 'kableExtra', 'testthat', 'covr', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

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:
  'readxl', 'dplyr', 'stringr', 'lubridate', 'magrittr', 'tibble',
  'zoo', 'purrr', 'tidyr', 'broom', 'cli', 'ggplot2', 'glue',
  'minpack.lm', 'patchwork', 'rlang', 'usethis', 'nlstools', 'pillar'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'fansi', 'collapsibleTree', 'testthat',
  'shiny', 'miniUI', 'datapasta', 'rstudioapi', 'htmltools', 'readr',
  'anomalize', 'ggforce', 'ggtext', 'forcats', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'markdown'
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'raster', 'rgdal'

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: 'plyr', 'igraph'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'corpcor'

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: 'oro.nifti', 'neurobase'

Packages suggested but not available 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'

Packages suggested but not available for checking:
  'covr', 'mockery', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'tibble', 'tidyr', 'Rcpp', 'vcfR', 'viridis',
  '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:
  'psych', 'colorspace', 'dplyr', 'eRm', 'ggraph', 'ggplot2',
  'GPArotation', 'httr', 'igraph', 'intergraph', 'lordif', 'lubridate',
  'nFactors', 'openxlsx', 'plyr', 'polycor', 'purrr', 'RColorBrewer',
  'readr', 'rlang', 'scales', 'srvyr', 'stringr', 'survey', 'TAM',
  'tibble', 'tidygraph', 'tidyr', 'WrightMap'

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.
Packages required but not available:
  'data.table', 'magrittr', 'openxlsx', 'dplyr', 'purrr', 'bit64'

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:
  'abind', 'data.table', 'shiny', 'dplyr', 'DT'

Packages suggested but not available for checking:
  'dplR', 'imager', 'jsonlite', 'jpeg', 'png', 'plotly', 'shinyFiles',
  'shinyjs', 'shinythemes', 'raster', 'rgdal', 'readr', 'readxl', 'sp',
  'testthat', 'tiff', 'tibble', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'snowfall'

Package suggested but not available for checking: 'SSsimple'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'htmltools', 'purrr', '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:
  'rlang', 'dplyr', 'tidyr', 'reshape2', 'tidytext', 'purrr', 'broom',
  'tibble', 'gapminder'

Packages suggested but not available for checking:
  'ggraph', 'igraph', 'testthat', 'covr', 'knitr', 'janeaustenr',
  'rmarkdown', 'unvotes', 'countrycode', 'fuzzyjoin', 'ggplot2',
  'maps', 'irlba'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'xml2', 'stringr', 'stringi', 'readr', 'jsonlite', 'keyring'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'stringr', 'tibble'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages required but not available:
  'httr', 'dplyr', 'jsonlite', 'WikipediR', 'ratelimitr', 'purrr',
  'readr', 'rex'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'WikipediR', 'WikidataQueryServiceR', 'tibble',
  'dplyr', 'stringr', 'Hmisc', 'progress', 'pbapply', 'readr', 'crayon'

Packages suggested but not available for checking:
  'markdown', 'testthat', 'tidyverse', 'knitr', 'pageviews'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'rvest', 'xml2'

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:
  'maps', 'rvest', 'stringi', 'WikipediR', 'xml2', 'sp', 'stringr',
  'selectr', 'units', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', '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: 'XML', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pageviews', 'stringr', 'rvest', 'httr', 'xml2', 'hellno', 'glue',
  'ggplot2'

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: 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'WikidataR', 'pageviews'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'WikidataR', 'data.table', 'curl', 'crul', 'tibble', 'jsonlite',
  'xml2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', '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:
  'WikidataQueryServiceR', 'WikidataR', 'httr', 'jsonlite',
  'ratelimitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
wilcox.selection.split: no visible global function definition for
  'pnorm'
wilcox.test2: no visible global function definition for 'wilcox.test'
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magrittr', '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:
  'adehabitatLT', 'dplyr', 'rgeos', 'sf', 'sp'

Packages suggested but not available for checking:
  'adehabitatHR', 'ggplot2', 'GGally', 'igraph', 'network', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clubSandwich', 'sandwich', 'robumeta', 'metafor'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'covr', 'mockery'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'dplyr', 'httr', 'jsonlite', 'lubridate', 'purrr', 'rnoaa',
  'RSQLite', 'shiny', 'tibble', 'tidyr', 'shinythemes', 'ggplot2',
  'plotly', 'ggthemes'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', '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', 'data.table', 'ggplot2', 'plotly', 'scales',
  'shinydashboard', 'DT', 'colourpicker', 'RColorBrewer', 'shinyjs',
  'viridis', 'rje', 'plyr', 'circlize', 'ComplexHeatmap', 'gplots',
  'reshape', 'rintrojs', 'RJSONIO', 'ggrepel', 'DESeq2', 'rjson',
  'FactoMineR', 'factoextra', 'heatmaply', 'shinycssloaders', 'log4r',
  'openssl', 'R6', 'zip', 'shinyWidgets'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'stringi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'procmaps'

Packages suggested but not available for checking:
  'DBI', 'knitr', 'magrittr', 'purrr', 'rlang', 'rmarkdown', 'RSQLite',
  'testthat', 'vctrs'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readbitmap', 'drc', 'imputeTestbench'

Packages suggested but not available 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:
  'geiger', 'ape', 'phangorn', 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'ggplot2', 'tidyr', 'curl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sampling'

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', 'utf8', 'rnrfa', 'httr', 'jsonlite', 'curl', 'knitr',
  'rmarkdown', 'zoo'

VignetteBuilder 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:
  'plyr', 'lubridate', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'pssm', 'MLEcens', 'data.table', 'JM', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'Rcpp', 'dplyr', 'magrittr', 'tidyselect'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'copula', 'ggplot2', 'ggpubr', 'reshape2', 'stringr', 'viridis'

Packages suggested but not available 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:
  'HDInterval', 'mcmcOutput', 'truncnorm', 'coda', 'plotrix'

Packages suggested but not available for checking: 'secr', 'shiny', 'rjags'

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: 'MASS'
  All declared Imports should be used.
Running 'testthat.R'
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:
  'Rgraphviz', 'RBGL', 'graph', 'bnlearn', 'HydeNet', 'rhandsontable',
  'shiny', 'shinydashboard', 'dplyr', 'visNetwork', 'shinyWidgets',
  'missRanger', 'shinyalert', 'shinycssloaders', 'rintrojs', 'arules',
  'psych', 'DescTools', 'DT', 'linkcomm', 'igraph', 'shinyBS'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rcompanion'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'callr', 'covr', 'DBI', 'knitr', 'rlang', 'rmarkdown', 'RSQLite',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'withr-Ex.R' failed
The error most likely occurred in:

> ### Name: with_db_connection
> ### Title: DBMS Connections which disconnect themselves.
> ### Aliases: with_db_connection local_db_connection
> 
> ### ** Examples
> 
> db <- tempfile()
> with_db_connection(
+   list(con = DBI::dbConnect(RSQLite::SQLite(), db)), {
+     DBI::dbWriteTable(con, "mtcars", mtcars)
+ })
Error in loadNamespace(x) : there is no package called 'DBI'
Calls: with_db_connection ... 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: 'sp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'infotheo', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'vctrs', 'sf', 'tibble', 'readr'
Packages unavailable to check Rd xrefs: 'sf', 'vctrs'
Running examples in 'wk-Ex.R' failed
The error most likely occurred in:

> ### Name: wk_plot
> ### Title: Plot well-known geometry vectors
> ### Aliases: wk_plot wk_plot.default plot.wk_wkt plot.wk_wkb plot.wk_xy
> ###   plot.wk_rct plot.wk_crc
> 
> ### ** Examples
> 
> plot(as_wkt("LINESTRING (0 0, 1 1)"))
Error: Package 'vctrs' is required for wk_plot()
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: 'wk', 'Rcpp', 'tibble', '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: 'genlasso', 'tibble', 'ggplot2'

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:
  'LindleyR', 'pracma', 'nleqslv', 'goftest', 'cubature', 'bbmle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'inline'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dbayes: no visible global function definition for 'mahalanobis'
dbayes: no visible global function definition for 'var'
wmd: no visible global function definition for 'cor'
wmd: no visible global function definition for 'var'
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
Package required but not available: 'waveslim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', '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
Packages required but not available: 'lamW', 'smoothmest'

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: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'pscl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'msm', 'mvtnorm', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'coda', 'classInt', '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:
  'covr', 'lintr', '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:
  'scales', 'dplyr', 'rlang', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'magrittr', 'pander', 'rmarkdown', 'testthat',
  'tidyselect', 'utf8'

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', 'quantmod', 'rmarkdown', 'stargazer', 'tinytest', 'xts',
  'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'rmarkdown', 'prereg', 'gert', 'ranger', 'yaml', 'digest', 'rticles'

Packages suggested but not available for checking:
  'remotes', 'tinytex', 'renv', 'knitr', 'missRanger', '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', 'RcppProgress'

Package suggested but not available for checking: 'udpipe'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'openxlsx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'DBI', 'dbplyr', 'dplyr', 'purrr', 'quantregGrowth',
  'rlang', 'RMySQL', 'robustbase', 'stringr', 'tidyr'

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: 'htmlwidgets', 'base64enc'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'webshot'

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: 'RColorBrewer', 'Rcpp'

Packages suggested but not available for checking: 'tm', 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidygraph', 'tibble', 'plyr', 'ggraph', 'purrr', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crayon'

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: 'plyr', 'reshape2'

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.
Package required but not available: 'LambertW'

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:
  'dlr', 'fastmatch', 'memoise', 'piecemaker', 'rlang', 'stringi',
  'wordpiece.data'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dplyr'
Packages required but not available:
  'digest', 'ggplot2', 'patchwork', 'stringr', 'dplyr', 'SnowballC'

Packages suggested but not available for checking:
  'testthat', 'covr', '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:
  'dplyr', 'officer', 'flextable', 'xml2'

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:
  'tibble', 'text2vec', 'word2vec', 'fastTextR'

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', 'sparsesvd', 'iotools'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tm', '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', 'dplyr', 'generics', 'purrr', 'rlang', 'rsample',
  'tibble', 'tidyr', 'vip', 'workflows'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'recipes', 'rmarkdown', 'testthat', 'tidymodels',
  'tune', '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:
  'callr', 'fs', 'getPass', 'git2r', 'glue', 'httpuv', 'httr', 'knitr',
  'rmarkdown', 'rprojroot', 'rstudioapi', 'stringr', 'whisker', 'xfun',
  'yaml'

Packages suggested but not available for checking:
  'clipr', 'covr', 'devtools', 'miniUI', 'reticulate', 'shiny',
  'spelling', 'testthat', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'generics', 'ggplot2', 'hardhat', 'lifecycle',
  'prettyunits', 'purrr', 'rlang', 'rsample', 'tibble', 'tidyr',
  'tune', 'vctrs', 'withr', 'workflows'

Packages suggested but not available for checking:
  'covr', 'dials', 'kknn', 'knitr', 'modeldata', 'parsnip', 'recipes',
  'rmarkdown', 'spelling', 'testthat', 'yardstick'

VignetteBuilder 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', 'generics', 'glue', 'hardhat', 'lifecycle', 'parsnip',
  'rlang', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'butcher', 'covr', 'dials', 'knitr', 'magrittr', 'modeldata',
  'recipes', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pracma', 'signal'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr', 'ggplot2', 'magrittr',
  'purrr', 'tidyr'

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: 'data.table', 'stringr'
Package unavailable to check Rd xrefs: 'stringr'
Note: found 2 marked UTF-8 strings
Running examples in 'WorldFlora-Ex.R' failed
The error most likely occurred in:

> ### Name: WFO.match
> ### Title: Standardize plant names according to World Flora Online
> ###   taxonomic backbone
> ### Aliases: WFO.match WFO.url WFO.one WFO.browse WFO.synonyms WFO.family
> 
> ### ** Examples
> 
> 
> data(WFO.example)
> 
> spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida",
+     "Omalanthus populneus", "Pygeum afric"))
> 
> WFO.match(spec.data=spec.test, WFO.data=WFO.example, counter=1, verbose=TRUE)
Loading required namespace: data.table
Failed with error:  'there is no package called 'data.table''
Error in WFO.match(spec.data = spec.test, WFO.data = WFO.example, counter = 1,  : 
  Please install the data.table package
Execution halted
Packages required but not available:
  'dplyr', 'glue', 'janitor', 'jsonlite', 'lubridate', 'magrittr',
  'progress', 'purrr', 'qdapRegex', 'readr', 'rlang', 'rvest',
  'stringi', 'stringr', 'tidyr', 'withr', 'xml2', '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:
  'openair', 'doParallel', 'foreach', 'purrr', 'dplyr', 'leaflet',
  'tidyr', 'readr'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'tibble', 'jsonlite', 'data.table'

Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown', 'testthat', '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: 'httr', 'xml2', 'jsonlite', 'pbapply'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr'

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', 'tidyselect', 'magrittr', 'purrr', 'reshape2',
  'ggplot2', 'ggrepel', 'scales', 'htmltools', 'markdown', 'rmarkdown',
  'networkD3', 'DT', 'tidytext', 'ggraph', 'igraph', 'proxy',
  'ggwordcloud', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'extrafont', 'leiden', 'lifecycle', 'fst', 'glue',
  'flexdashboard', 'lmtest', 'portes', 'sandwich'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mvtnorm'
'LazyData' is specified without a 'data' directory
Running examples in 'WPKDE-Ex.R' failed
The error most likely occurred in:

> ### Name: findPeak
> ### Title: find peaks
> ### Aliases: findPeak
> ### Keywords: peak
> 
> ### ** Examples
> 
> data.gen<-function(n.peaks=100, N=1e5, max.var=0.001, max.corr=0.5)
+ {
+   library(mvtnorm)
+ 
+   dat<-matrix(0, nrow=N, ncol=2)
+   all.m<-c(NA,NA)
+ 
+   for(i in 1:n.peaks)
+   {
+     this.m<-runif(2)
+     this.var<-runif(2, min=0.1*max.var, max=max.var)
+     this.cov<-runif(1, min=-1*max.corr, max=max.corr) * sqrt(this.var[1])* sqrt(this.var[2])
+     this.s<-matrix(c(this.var[1], this.cov, this.cov, this.var[2]),ncol=2)
+ 
+     dat[((i-1)*N/n.peaks+1):(i*N/n.peaks),]<-rmvnorm(N/n.peaks, mean=this.m, sigma=this.s)
+     all.m<-rbind(all.m, this.m)
+   }
+ 
+   all.m[,1]<-(all.m[,1]-min(dat[,1]))/diff(range(dat[,1]))
+   all.m[,2]<-(all.m[,2]-min(dat[,2]))/diff(range(dat[,2]))
+   dat[,1]<-(dat[,1]-min(dat[,1]))/diff(range(dat[,1]))
+   dat[,2]<-(dat[,2]-min(dat[,2]))/diff(range(dat[,2]))
+ 
+   all.m<-all.m[-1,]
+   return(list(dat=dat,m=all.m))
+ }
> 
> 
> r<-data.gen(n.peaks=100, N=1e5, max.var=0.001, max.corr=0.5)
Error in library(mvtnorm) : there is no package called 'mvtnorm'
Calls: data.gen -> library
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages unavailable to check Rd xrefs: 'wpp2010', 'wpp2012'
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'plyr'

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.
Packages required but not available:
  'shiny', 'shinythemes', 'shinyjs', 'plyr', 'reshape2', 'googleVis',
  'wpp2019', 'Hmisc', 'ggplot2', 'DT'

Packages suggested but not available for checking:
  'wpp2017', 'wpp2015', 'wpp2012', 'wpp2010', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2', '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: 'Rsolnp', 'glm2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'magrittr', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'knitr', 'coin', 'dplyr', 'forcats', 'purrr', 'glue',
  'rlang', 'stringr', 'magrittr', 'ggplot2', 'tibble', 'tidyr',
  'kableExtra'

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', 'rmarkdown', 'R.rsp', 'tinytest'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'compare', '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: 'RColorBrewer', 'wrMisc'

Packages suggested but not available for checking:
  'dplyr', 'factoextra', 'FactoMineR', 'knitr', 'limma', 'rmarkdown',
  'sm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fdapace', 'fdadensity', 'Rfast', 'CVXR', 'expm', 'ggplot2',
  'gridExtra', 'Rcpp', 'locfit', 'mvtnorm', 'locpol', 'modeest',
  'rlang', '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.
Malformed Title field: should not end in a period.
Packages suggested but not available for checking:
  'spelling', 'readxl', 'nycflights13', 'testthat', 'bit64'
Running examples in 'writexl-Ex.R' failed
The error most likely occurred in:

> ### Name: write_xlsx
> ### Title: Export to xlsx
> ### Aliases: write_xlsx writexl
> 
> ### ** Examples
> 
> # Roundtrip example with single excel sheet named 'mysheet'
> tmp <- write_xlsx(list(mysheet = iris))
> readxl::read_xlsx(tmp)
Error in loadNamespace(x) : there is no package called 'readxl'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'spelling.R'
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'BBmisc', 'coin', 'data.table', 'data.tree', 'fdrtool', 'flexclust',
  'knitr', 'limma', 'markdown', 'mixdist', 'NbClust', 'preprocessCore',
  'qvalue', 'Rcpp', 'RColorBrewer', 'readxl', 'rmarkdown', 'som',
  'stringi', 'VGAM', 'vsn', 'wrGraph'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'data.tree', 'coin', 'limma', 'vsn', 'fdrtool', 'cranlogs', 'packageRank', 'flexclust', 'data.table', 'readxl', 'wrGraph'
Running examples in 'wrMisc-Ex.R' failed
The error most likely occurred in:

> ### Name: buildTree
> ### Title: Connect edges to from tree and extract all possible branches
> ### Aliases: buildTree
> 
> ### ** Examples
> 
> frag2 <- cbind(beg=c(2,3,7,13,13,15,7,9,7,3,7,5,7,3),end=c(6,12,8,18,20,20,19,12,12,4,12,7,12,4)) 
> rownames(frag2) <- c("A","E","B","C","D","F","H","G","I", "J","K","L","M","N")
> buildTree(frag2)
Error in loadNamespace(x) : there is no package called 'data.tree'
Error in buildTree(frag2) : 
   -> buildTree : : Problem running package data-tree : Can't even create a new generic node
Execution halted
Packages required but not available: 'knitr', 'limma', 'wrMisc'

Packages suggested but not available for checking:
  'data.table', 'fdrtool', 'RColorBrewer', 'readxl', 'ROTS',
  'rmarkdown', 'R.utils', 'sm', 'wrGraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cubature', 'gumbel'

Packages suggested but not available 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: 'reshape', 'plyr', 'mc2d'

Packages suggested but not available for checking:
  'knitr', 'car', 'ggplot2', 'colorspace', 'mediation', 'GGally'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/WRS2.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Hmisc', 'nloptr', 'ggplot2', 'GGally', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'logging', 'Rcpp'

Packages suggested but not available for checking:
  'BatchExperiments', 'BiocManager', 'dplyr', 'ggplot2', 'import',
  'kimisc', 'knitcitations', 'knitr', 'metap', 'microbenchmark',
  'rmarkdown', 'roxygen2', 'rticles', 'sampling', 'testthat', 'tidyr',
  'tikzDevice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'caret', 'dplyr', 'fields', 'foreach', 'forecast',
  'gridExtra', 'lubridate', 'purrr', 'quantreg', 'RColorBrewer',
  'tidyr'

Packages suggested but not available for checking:
  'doParallel', 'EGRET', 'magrittr', 'plotly', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'wrMisc', 'wrProteo'

Packages suggested but not available for checking:
  'BiocParallel', 'data.tree', 'fdrtool', 'knitr', 'limma',
  'preprocessCore', 'RColorBrewer', 'rmarkdown', 'wrGraph'

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: 'devtools'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'transport', 'RSpectra', 'expm', 'plot3D', 'imager',
  'lpSolve', 'RcppArmadillo'

Packages suggested but not available for checking:
  'magick', 'mvtnorm', 'Rsymphony'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'magrittr', 'stringr', 'scales', '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: 'latticeExtra', 'fpc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'mnormt'

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', 'randomForest', 'stringr', '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: 'fields'

Packages suggested but not available for checking:
  'knitr', 'mvtnorm', 'rmarkdown', 'testthat', 'vdiffr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'igraph', 'magrittr', 'plyr', 'som', 'visNetwork',
  '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.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'httr', 'jsonlite', 'dplyr'

Packages suggested but not available for checking:
  'roxygen2', '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:
  'sp', 'ncdf4', 'reshape', 'abind', 'fields', 'rgdal', 'rgeos',
  'stringr', 'Hmisc', 'gdata', 'corpcor', 'rworldmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'wrapr', 'ggplot2', 'sigr', 'cdata', 'rqdatatable', 'rquery',
  'gridExtra'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plotly', 'hexbin', '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', 'simts', 'coda', 'RcppArmadillo'

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: 'tiff'
Packages required but not available: 'sde', 'ftsa', 'rainbow'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'fOptions', 'CompQuadForm',
  'tensorA'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'inline'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'tidyr', 'wyz.code.offensiveProgramming', '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:
  'data.table', 'tidyr', 'stringr', 'R6', '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:
  'data.table', 'tidyr', 'wyz.code.offensiveProgramming', 'stringr',
  'R6', 'crayon', '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:
  'data.table', 'tidyr', 'wyz.code.offensiveProgramming', 'R6'

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: 'x13binary', 'stringr'

Packages suggested but not available for checking: 'covr', 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'xml2', 'rgl', 'zoo', 'png', 'readr', 'dplyr', 'pracma',
  'assertthat'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'here', 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'knitr', 'servr', 'xfun', 'rmarkdown'

Packages suggested but not available for checking: 'rstudioapi', 'testit'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colorspace', 'glue', 'purrr', 'whisker'

Packages suggested but not available for checking:
  'callr', 'ggplot2', 'knitr', 'mockery', 'rmarkdown', 'scales',
  'showtext', 'sysfonts', 'testthat', 'xaringan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BGLR'

Packages suggested but not available 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', 'nlshrink', 'RcppArmadillo'

Package suggested but not available for checking: 'rugarch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'xtable', 'jsonlite', 'ggplot2', 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ergm', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bupaR', 'dplyr', 'XML', 'xml2', 'data.table', 'tidyr', 'purrr',
  'stringr', '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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testit', 'rstudioapi', 'tinytex', 'mime', 'markdown', 'knitr',
  'htmltools', 'remotes', 'pak', 'rhub', 'renv', 'curl', 'jsonlite',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'remotes'
Running examples in 'xfun-Ex.R' failed
The error most likely occurred in:

> ### Name: base64_uri
> ### Title: Generate the Data URI for a file
> ### Aliases: base64_uri
> 
> ### ** Examples
> 
> logo = xfun:::R_logo()
> img = htmltools::img(src = xfun::base64_uri(logo), alt = "R logo")
Error in loadNamespace(x) : there is no package called 'htmltools'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'test-ci.R'
  Running 'test-cran.R'
Running the tests in 'tests/test-cran.R' failed.
Complete output:
  > testit::test_pkg('xfun', 'test-cran')
  Error in loadNamespace(x) : there is no package called 'testit'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'xgboost', 'data.table'

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: 'data.table', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'DiagrammeR', 'Ckmeans.1d.dp',
  'vcd', 'testthat', 'lintr', 'igraph', 'float', 'crayon', 'titanic'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/xgboost.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'binom', 'Deriv', 'DescTools', 'dplyr', 'ggplot2',
  'glue', 'gtable', 'Hmisc', 'labeling', 'magrittr', 'minpack.lm',
  'pander', 'png', 'RCurl', 'readr', 'scales', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'caTools', 'gridExtra', 'knitr', 'pkgdown', 'rmarkdown', 'testthat',
  'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
XHWE: no visible global function definition for 'read.table'
result: no visible global function definition for 'pchisq'
result: no visible global function definition for 'rbinom'
result: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package required but not available: 'psychTools'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

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:
  > # the tests are realized using the "testthat" package
  > # and can be found in ./testthat
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_check("XiMpLe")
  Error in test_check("XiMpLe") : could not find function "test_check"
  Execution halted
Package required but not available: 'FNN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'magrittr', 'tibble', 'dplyr', 'jsonlite', 'glue',
  'htmltools', 'assertthat'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'extrafont', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rJava'

Packages suggested but not available for checking:
  'RUnit', 'ggplot2', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'abind', 'corpcor', 'igraph', 'capushe', 'glmnet', 'randomForest',
  'e1071', 'mda', 'progress'

Package suggested but not available for checking: 'shock'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mpoly'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'openxlsx'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rJava'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rJava', 'xlsxjars'

Packages suggested but not available for checking:
  'rprojroot', 'testthat', 'covr', 'tibble', 'knitr', 'rmarkdown'

VignetteBuilder 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', 'readxl'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotrix', 'aod', 'glmmML', 'numDeriv', 'metafor', 'mvmeta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'RUnit', 'data.table'
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'curl', 'httr', 'knitr', 'magrittr', 'mockery', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'curl', 'httr'
Running 'testthat.R'
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:
  'xml2', 'stringr', 'tidyr', 'fs', 'lubridate', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'XML', 'RCurl', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'stringr', 'readr', 'tibble', 'httr', 'lubridate'

Package suggested but not available for checking: 'xlsx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'testthat', 'xml2'
'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: 'bitops', 'RCurl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! xmlSApply(node, function(x)
 []

[142] [143]
Package textcomp Info: Symbol \textasciigrave not provided by
Packages required but not available: 'curl', 'xml2', 'base64enc'

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:
  'dplyr', 'tidyr', 'ggplot2', 'purrr', 'rlang', 'tibble', 'qpdf'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ChemmineR', 'covr', 'fmcsR'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'qtl'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'processx'

Packages suggested but not available for checking: 'ps', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clipr', 'checkmate', 'dplyr', 'fansi', 'lifecycle', 'plyr', 'rlang',
  'rstudioapi', 'testthat', 'tibble', 'withr'

Packages suggested but not available for checking:
  'data.table', 'knitr', 'rmarkdown'

VignetteBuilder 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', 'readr', 'RCurl', 'httr'

Package suggested but not available for checking: 'car'

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:
  'blorr', 'data.table', 'descriptr', 'DT', 'haven', 'highcharter',
  'jsonlite', 'kableExtra', 'magrittr', 'olsrr', 'plotly', 'rbokeh',
  'readr', 'readxl', 'rfm', 'shinyBS', 'shinycssloaders',
  'shinythemes', 'vistributions'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FactoMineR', 'ggplot2', 'tm', 'ggdendro', 'ggforce', 'ggrepel',
  'gridExtra', 'stringi', 'stringr', 'slam', 'flexclust', 'flashClust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Hmisc', 'dplyr', 'tibble', 'lazyeval', 'gam', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xpose', 'ggplot2', 'nlmixr', 'dplyr', 'tibble', 'stringr', 'tidyr',
  'magrittr', 'vpc', 'crayon', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggforce', 'purrr', 'readr', 'rlang', 'stringr',
  'tibble', 'tidyr', 'vpc'

Packages suggested but not available for checking:
  'here', 'gridExtra', 'rmarkdown', 'knitr', 'testthat', 'plotly',
  'webshot', '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:
  'dplyr', 'scales', 'foreach', 'ggplot2', 'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'xgboost', 'dplyr', 'fuzzyjoin', 'rlang'

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: 'XR'

Packages suggested but not available 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', 'foreach', 'bigmemory', 'RcppEigen', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colourpicker', 'data.table', 'jpeg', 'lubridate', 'moments',
  'RCurl', 'raster', 'rgdal', 'rjson', 'sp', 'stringr', 'tiff',
  'shiny', 'shinyjs'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'shinyBS', 'shinyAce', 'shinyTime',
  'shinyFiles', 'shinydashboard', 'shinythemes', '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: 'XR', 'reticulate'

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: 'xml2', '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:
  'pdp', 'dplyr', 'ggplot2', 'magrittr', 'purrr', 'tidyr', 'pROC'

Packages suggested but not available for checking:
  'ALEPlot', 'factorMerger', 'testthat', 'knitr', 'rmarkdown',
  'ResourceSelection', 'randomForest', 'e1071', 'caret', 'breakDown',
  'DALEX', 'xgboost', 'gridExtra', 'ISLR'

VignetteBuilder 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', '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: 'countrycode', 'haven', 'RCurl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'plm', 'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/OtherPackagesGallery.Rnw'
   'inst/doc/listOfTablesGallery.Rnw'
   'inst/doc/margintable.Rnw'
   'inst/doc/xtableGallery.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/OtherPackagesGallery.Rnw'
   'vignettes/listOfTablesGallery.Rnw'
   'vignettes/margintable.Rnw'
   'vignettes/xtableGallery.Rnw'
(Is a VignetteBuilder field missing?)
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 unavailable to check Rd xrefs: 'RColorBrewer'
Package required but not available: 'pracma'

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.
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("zoo"): there is no package called 'zoo'

See section 'Package namespaces' in the 'Writing R Extensions' manual.
Packages required but not available: 'glmnet', 'selectiveInference'

Packages suggested but not available for checking:
  'knitr', 'numDeriv', 'lbfgs', '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: 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'rmarkdown', 'textutils', 'bench', 'xml2',
  '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: 'SACCR', 'Trading'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'glpkAPI', 'lpSolveAPI', 'reshape2'

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 suggested but not available for checking: 'RSpectra'
Package unavailable to check Rd xrefs: 'RSpectra'
Packages required but not available: 'foreach', 'pheatmap', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randtoolbox', 'lhs', 'MLmetrics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'vegan', 'ccaPP', 'randomForest', 'gam', 'fastICA', 'gower'
Packages unavailable to check Rd xrefs: 'gam', 'randomForest', 'fastICA', 'vegan', 'gower', 'ccaPP'
Running examples in 'yaImpute-Ex.R' failed
The error most likely occurred in:

> ### Name: applyMask
> ### Title: Removes neighbors that share (or not) group membership with
> ###   targets.
> ### Aliases: applyMask
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> require (yaImpute)
> 
> data(iris)
> 
> # build a base case, there are no targets, 
> #    turn off getting references neighbors.
> mal <- yai(x=iris[,-5],method="mahalanobis", noRefs = TRUE)
> 
> # create a new data, just a copy of the old with new row names.
> iris2 <- iris
> rownames(iris2) <- paste0("new.",rownames(iris))
> 
> # do an imputation with k=55
> m55 <- newtargets(mal,newdata=iris2,k=55)
Error in loadNamespace(x) : there is no package called 'gower'
Calls: newtargets ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'Rcpp', 'checkmate', 'BBmisc'

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: 'foreach', 'iterators'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'yaml', 'csv', 'encode', 'units', 'spork', 'ggplot2', 'dplyr',
  'rlang', 'xtable', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'magrittr', 'table1', 'knitr', 'rmarkdown', '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:
  'covr', 'devtools', 'knitr', 'rmarkdown', 'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # browseURL("https://kbroman.org/pkg_primer/pages/tests.html")
  > # browseURL(file.path("https://walczak.org/2017/06",
  > # 		"how-to-add-code-coverage-codecov-to-your-r-package/"))
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: 'RUnit'
Running 'RUnit.R'
Running the tests in 'tests/RUnit.R' failed.
Complete output:
  > stopifnot(require(RUnit, quietly=TRUE))
  Error: require(RUnit, quietly = TRUE) is not TRUE
  Execution halted
Packages required but not available: 'depth', 'OjaNP', 'pcaPP', 'interp'

Package suggested but not available for checking: 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randtoolbox', 'lhs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'circular', 'cowplot', 'data.table', 'ggplot2', 'ggrepel', 'nloptr',
  'plyr', 'Rcpp', 'reshape2', 'splusTimeSeries', 'tictoc', 'TMB',
  'viridis', 'zoo', 'RcppEigen'

Packages suggested but not available for checking:
  'caTools', 'covr', 'knitr', 'rmarkdown', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'generics', 'pROC', 'rlang', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'covr', 'crayon', 'ggplot2', 'knitr', 'probably', 'purrr',
  'rmarkdown', 'testthat', 'tidyr'

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: 'jpeg', 'BayesFactor', 'circlize'

Packages suggested but not available 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', 'purrr', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'ggtree', 'knitr', '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: 'lubridate'

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: 'yacca', 'miscTools', 'plotrix'

Package suggested but not available for checking: 'MBESS'

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.
Package required but not available: 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'foreach'

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: '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:
  'crayon', 'fs', 'glue', 'magrittr', 'miniUI', 'purrr', 'rlang',
  'rmarkdown', 'rstudioapi', 'shiny', 'shinyBS', 'stringr', 'usethis',
  'whoami', 'withr', 'yaml'

Packages suggested but not available for checking:
  'blogdown', 'bookdown', 'covr', 'knitr', 'pkgdown', 'prettydoc',
  'roxygen2', 'spelling', 'testthat', 'xaringan'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'htmltools', 'magrittr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'reshape2', 'yaml', 'gridExtra', 'rpart.plot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'lifecycle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'writexl', 'reticulate', 'purrr', 'magrittr', 'tibble',
  'dplyr'

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.
Package required but not available: 'tsibble'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'markdown', 'rmarkdown', 'dplyr', 'tidyr',
  'forcats', 'janitor', '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:
  'Formula', 'Rcpp', 'rstan', 'rstantools', 'BH', 'RcppEigen',
  'StanHeaders'

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: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Formula', 'Rcpp', 'rstan', 'rstantools', 'BH', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'chk', 'ggplot2', 'lifecycle', 'purrr', 'scales', 'yesno'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'rstudioapi', '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:
  'spelling', 'dplyr', 'readxl', 'stringr', 'eulerr', 'Peptides',
  'svDialogs'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'shinyjs', 'shiny', 'shinydashboard', 'shinyBS', 'yuima',
  'quantmod', 'sde', 'ggplot2', 'plotly', 'ghyp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'expm', 'cubature', 'mvtnorm', 'Rcpp', 'glassoFast', 'coda',
  'calculus', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgbuild'
Packages required but not available: 'httr', 'jsonlite'

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: 'yaml'

Packages suggested but not available for checking:
  'covr', 'data.tree', 'here', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjson', 'stringr', 'magrittr', 'lubridate', 'dplyr'

Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa', 'neonUtilities'

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', 'fitdistrplus'

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', 'tibble'

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: 'NADA', 'truncnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'nleqslv', 'evmix', 'Rdpack'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'jsonlite', 'purrr', 'httr', 'tidyr', 'plyr'

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', 'purrr', 'magrittr'

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: 'triangle', 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'foreach', 'iterators', 'reshape2', 'plyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'devtools', '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:
  'behavr', 'data.table', 'lomb', 'pracma', 'WaveletComp'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'ggetho', 'damr', 'xsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'httr', 'jsonlite', 'xml2', 'keyring'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', 'rjson'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'loon', 'graph', 'PairViz'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Rgraphviz', 'ADGofTest', 'copula', 'pcaPP',
  'qqtest', 'qrmdata', 'qrmtools', 'rugarch', 'zoo', 'ggplot2',
  'gridExtra', 'scagnostics', 'testthat'

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: 'ppcor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'scam', 'car', 'vegan', 'Imap', 'nnls', 'glm2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'SKAT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'estimatr'
Running examples in 'zfit-Ex.R' failed
The error most likely occurred in:

> ### Name: zfitter
> ### Title: Create a pipe-friendly version of a given fitting function
> ### Aliases: zfitter
> 
> ### ** Examples
> 
> 
> zlm_robust <- zfitter(estimatr::lm_robust)
Error in loadNamespace(x) : there is no package called 'estimatr'
Calls: zfitter ... 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: 'mcc'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gamlss', 'gamlss.dist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'coda', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', 'XML'

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: 'pscl', 'TSA'
Packages unavailable to check Rd xrefs: 'pscl', 'dplyr', 'TSA'
Packages required but not available:
  'dplyr', 'lifecycle', 'lubridate', 'magrittr', 'memoise', 'purrr',
  'rlang', 'stringi', 'stringr', 'tibble', 'arabic2kansuji'

Packages suggested but not available for checking:
  'covr', 'testthat', 'scales'

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:
  'rlang', 'stringr', 'raster', 'tidycensus', 'tidyr', 'dplyr',
  'jsonlite', 'httr', 'curl', 'RSQLite', 'DBI'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'readr', 'testthat', '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:
  'doParallel', 'foreach', 'optimx', 'trustOptim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'VGAM', 'tolerance', 'copula'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 146804 marked UTF-8 strings
Packages required but not available: 'Rcpp', 'pracma', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geosphere', 'magrittr', 'testthat', 'rlang', 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'processx', 'R6', 'testthat', 'withr'
Package unavailable to check Rd xrefs: 'processx'
Running examples in 'zip-Ex.R' failed
The error most likely occurred in:

> ### Name: unzip_process
> ### Title: Class for an external unzip process
> ### Aliases: unzip_process
> 
> ### ** Examples
> 
> ex <- system.file("example.zip", package = "zip")
> tmp <- tempfile()
> up <- unzip_process()$new(ex, exdir = tmp)
Error in need_packages(c("processx", "R6"), "creating unzip processes") : 
  The `processx` package is needed for creating unzip processes
Calls: unzip_process -> need_packages
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: 'rgenoud', 'purrr', 'data.table'

Packages suggested but not available for checking:
  'markdown', 'knitr', 'ggplot2', 'ggrepel', 'ggthemes', 'kableExtra',
  'stringr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  '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
Skipping vignette re-building
Packages suggested but not available for checking:
  'roxygen2', 'rmarkdown', 'testthat', 'tibble', 'dplyr', 'knitr',
  'desc', 'purrr', 'stringr', 'rprojroot'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'zmisc-Ex.R' failed
The error most likely occurred in:

> ### Name: lookup
> ### Title: Lookup values from a lookup table
> ### Aliases: lookup
> 
> ### ** Examples
> 
> fruit_lookup_vector <- c(a="Apple", b="Banana", c="Cherry")
> lookup(letters[1:5], fruit_lookup_vector)
[1] "Apple"  "Banana" "Cherry" "d"      "e"     
> 
> mtcars_lookup_data_frame <- data.frame(
+   name = c("mpg", "hp", "wt"),
+   value = c("Miles/(US) gallon", "Gross horsepower", "Weight (1000 lbs)"))
> lookup(names(mtcars), mtcars_lookup_data_frame)
Error in loadNamespace(x) : there is no package called 'tibble'
Calls: lookup ... 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: 'rjags', 'coda', 'Formula', 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gtools', 'compositions', 'Rcpp', 'RcppParallel', 'rstan',
  'rstantools', 'BH', 'RcppEigen', 'StanHeaders'

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', 'mockery', 'webmockr', 'base64url',
  'dplyr', 'MMWRweek', '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.
Packages required but not available:
  'ggplot2', 'RColorBrewer', 'raster', 'reshape2', 'rgdal'

Packages suggested but not available for checking:
  'knitr', 'rasterVis', 'rmarkdown', 'testthat', 'zdat'

VignetteBuilder 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', 'RColorBrewer'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tmap', 'tmaptools', 'pct', 'dplyr', 'lwgeom',
  'leaflet', 'covr', '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: 'ggplot2'

Packages suggested but not available for checking: 'rmarkdown', '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:
  'mlearning', 'svMisc', 'svDialogs', 'filehash', 'jpeg', 'png',
  'tiff', 'digest', 'mda', 'shiny', 'DT'

Packages suggested but not available for checking: 'rJava', 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringi', 'Rdpack'

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:
  'data.table', 'dplyr', 'lubridate', 'magick', 'openxlsx', 'paws',
  'pbapply', 'stringr', 'syuzhet'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Malformed Description field: should contain one or more complete sentences.
Running 'testall.R'
Running the tests in 'tests/testall.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'raster', 'dismo', 'plyr', 'randomForest', 'RCurl', 'rfigshare',
  'rgdal', 'roxygen2', 'rworldmap', 'sp', 'testthat'

Packages suggested but not available for checking:
  'knitr', 'maxlike', 'SDMTools'

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:
  'AER', 'coda', 'chron', 'fts', 'ggplot2', 'mondate', 'scales',
  'stinepack', 'strucchange', 'timeDate', 'timeSeries', 'tis',
  'tseries', 'xts'
Packages unavailable to check Rd xrefs: 'chron', 'fts', 'tseries', 'coda', 'tis', 'xts', 'ggplot2', 'stinepack'
Running 'as.Date.R'
Running the tests in 'tests/as.Date.R' failed.
Complete output:
  > ## set Z's timezone for reproducibility
  > Sys.setenv(TZ = "Europe/Vienna")
  > 
  > ## base results
  > as.Date(10957, origin = "1970-01-01")
  [1] "2000-01-01"
  > as.Date("2000-01-01")
  [1] "2000-01-01"
  > as.Date(as.POSIXct("2000-01-01 00:00:00 GMT", tz = "GMT"))
  [1] "2000-01-01"
  > as.Date(as.POSIXlt("2000-01-01 00:00:00 GMT", tz = "GMT"))
  [1] "2000-01-01"
  > as.Date(NA)
  [1] NA
  > 
  > ## for chron objects
  > library("chron")
  Error in library("chron") : there is no package called 'chron'
  Execution halted
Errors in running code in vignettes:
when running code in 'zoo-faq.Rnw'

> library("zoo")

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


> Sys.setenv(TZ = "GMT")

> suppressWarnings(RNGversion("3.5.0"))

> z <- suppressWarnings(zoo(1:8, c(1, 2, 2, 2, 3, 4, 
+     5, 5)))

> z
1 2 2 2 3 4 5 5 
1 2 3 4 5 6 7 8 

> aggregate(z, identity, mean)
  1   2   3   4   5 
1.0 3.0 5.0 6.0 7.5 

> aggregate(z, identity, tail, 1)
1 2 3 4 5 
1 4 5 6 8 

> time(z) <- na.approx(ifelse(duplicated(time(z)), NA, 
+     time(z)), na.rm = FALSE)

> z[!is.na(time(z))]
     1      2 2.3333 2.6667      3      4      5 
     1      2      3      4      5      6      7 

> Lines <- "1|BHARTIARTL|EQ|18:15:05|600|1\n2|BHARTIARTL|EQ|18:15:05|600|99\n3|GLENMARK|EQ|18:15:05|238.1|5\n4|HINDALCO|EQ|18:15:05|43.75|100\n5|BHART ..." ... [TRUNCATED] 

> library("zoo")

> library("chron")

  When sourcing 'zoo-faq.R':
Error: there is no package called 'chron'
Execution halted
when running code in 'zoo-quickref.Rnw'

> library("zoo")

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


> library("tseries")

  When sourcing 'zoo-quickref.R':
Error: there is no package called 'tseries'
Execution halted
when running code in 'zoo-read.Rnw'

> library("zoo")

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


> library("chron")

  When sourcing 'zoo-read.R':
Error: there is no package called 'chron'
Execution halted
when running code in 'zoo.Rnw'

> library("zoo")

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


> library("tseries")

  When sourcing 'zoo.R':
Error: there is no package called 'tseries'
Execution halted

  'zoo-design.Rnw'... OK
  'zoo-faq.Rnw'... failed
  'zoo-quickref.Rnw'... failed
  'zoo-read.Rnw'... failed
  'zoo.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'zoo-design.Rnw' using Sweave

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

--- finished re-building 'zoo-design.Rnw'

--- re-building 'zoo-faq.Rnw' using Sweave

Error: processing vignette 'zoo-faq.Rnw' failed with diagnostics:
 chunk 7 (label = duplicates) 
Error in library("chron") : there is no package called 'chron'

--- failed re-building 'zoo-faq.Rnw'

--- re-building 'zoo-quickref.Rnw' using Sweave

Error: processing vignette 'zoo-quickref.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("tseries") : there is no package called 'tseries'

--- failed re-building 'zoo-quickref.Rnw'

--- re-building 'zoo-read.Rnw' using Sweave

Error: processing vignette 'zoo-read.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("chron") : there is no package called 'chron'

--- failed re-building 'zoo-read.Rnw'

--- re-building 'zoo.Rnw' using Sweave

Error: processing vignette 'zoo.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("tseries") : there is no package called 'tseries'

--- failed re-building 'zoo.Rnw'

SUMMARY: processing the following files failed:
  'zoo-faq.Rnw' 'zoo-quickref.Rnw' 'zoo-read.Rnw' 'zoo.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'forecast', 'dygraphs'

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', 'knitr', 'rmarkdown', 'shinythemes', '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: 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'magrittr', 'RColorBrewer', 'flextable', 'officer',
  'rstudioapi', 'scales'

Packages suggested but not available for checking:
  'moonBook', '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:
  'DistributionUtils', 'Rcpp', 'mixtools', 'RcppEigen', 'RcppNumerical'

Packages suggested but not available for checking:
  'knitr', 'dplyr', 'ggplot2', 'rmarkdown', 'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'rvest', 'stringr', 'dplyr', 'ggplot2', 'lubridate',
  'assertthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'abind', 'mvtnorm', 'Rlinsolve', 'magrittr',
  'dplyr', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'partitions', 'ggplot2', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Kendall'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'httptest', 'roxygen2', '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
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘CVrej.ps’ ‘linhc.pdf’
'LazyData' is specified without a 'data' directory
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline lines par rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "text")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘acceldata2.RData’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for ‘pchisq’
print.linML: no visible global function definition for ‘pchisq’
print.loglinML: no visible global function definition for ‘pchisq’
print.satMarML: no visible global function definition for ‘pchisq’
print.satMcarWLS: no visible global function definition for ‘pchisq’
summary.funlinWLS: no visible global function definition for ‘pchisq’
summary.linML: no visible global function definition for ‘pchisq’
summary.loglinML: no visible global function definition for ‘pchisq’
summary.satMarML: no visible global function definition for ‘pchisq’
summary.satMcarWLS: no visible global function definition for ‘pchisq’
summary.waldTest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Aggregate: no visible global function definition for ‘aggregate’
Aggregate: no visible binding for global variable ‘tail’
Aggregate: no visible binding for global variable ‘var’
cocktailEnsemble: no visible global function definition for ‘glm’
cocktailEnsemble: no visible global function definition for ‘binomial’
cocktailEnsemble: no visible global function definition for ‘step’
cocktailEnsemble: no visible binding for global variable ‘na.omit’
imputeMissings : <anonymous>: no visible global function definition for
  ‘median’
predict.cocktailEnsemble: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

Rd file 'predict.cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
critical.values: no visible global function definition for ‘rnorm’
critical.values: no visible global function definition for ‘quantile’
mandel.test: no visible global function definition for ‘qf’
mtukey.test : p.test: no visible global function definition for ‘qf’
mtukey.test: no visible binding for global variable ‘quantile’
mtukey.test: no visible global function definition for ‘rnorm’
tukey.test: no visible global function definition for ‘qf’
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
Running ‘testthat.R’ [28s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("adjclust")
  > 
  > test_check("adjclust")
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 104 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • No NA value: nothing to test here! (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_ascendingCompatibility.R:34:3): snpClust gives results identical to those of adjclust 0.3.0 ──
  diag(ld.ceph) not identical to rep(0, p).
  names for target but not for current
  ── Failure (test_snpClust.R:39:3): 'snpClust' gives identical results regardless of data input format ──
  diag(ld.ceph) not identical to rep(0, p).
  names for target but not for current
  
  [ FAIL 2 | WARN 0 | SKIP 3 | PASS 104 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘About.Rmd’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘myplot.pdf’ ‘myplot.png’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
dke.fun.default: no visible global function definition for ‘hist’
kef: no visible global function definition for ‘dbinom’
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
plot.dke.fun: no visible global function definition for ‘hist’
plot.dke.fun: no visible global function definition for ‘lines’
plot.hcvc.fun1d: no visible global function definition for
  ‘plot.default’
plot.hcvd.fun1d: no visible global function definition for
  ‘plot.default’
plot.kern.fun1d: no visible global function definition for
  ‘plot.default’
plot.kpmfe.fun1d: no visible global function definition for
  ‘plot.default’
plot.reg.fun1d: no visible global function definition for
  ‘plot.default’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for ‘optim’
alabama: no visible global function definition for ‘optim’
auglag: no visible global function definition for ‘modifyList’
auglag1: no visible global function definition for ‘optim’
auglag1: no visible global function definition for ‘nlminb’
auglag2: no visible global function definition for ‘optim’
auglag2: no visible global function definition for ‘nlminb’
auglag3: no visible global function definition for ‘optim’
auglag3: no visible global function definition for ‘nlminb’
augpen: no visible global function definition for ‘optim’
constrOptim.nl: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
batch.possSpells.fnc: no visible binding for global variable ‘words’
possSpells.fnc: no visible binding for global variable ‘len.phons’
possSpells.fnc: no visible binding for global variable ‘phon1’
possSpells.fnc: no visible binding for global variable ‘len.total’
possSpells.fnc: no visible binding for global variable ‘poss.spells’
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Found the following files/directories:
  ‘more.words.rda’ ‘more.words.txt’ ‘more.words_log.txt’
  ‘other.words.rda’ ‘other.words.txt’ ‘other.words_log.txt’
  ‘some.words.rda’ ‘some.words.txt’ ‘some.words_log.txt’
  ‘yet.more.words.rda’ ‘yet.more.words.txt’ ‘yet.more.words_log.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
EXP.step: no visible global function definition for ‘rgamma’
EXP.step: no visible global function definition for ‘rnorm’
MAX.step: no visible global function definition for ‘uniroot’
Norm.GMedian: no visible binding for global variable ‘median’
RNASeq.Data.Gene: no visible binding for global variable ‘quantile’
decom.initial: no visible global function definition for ‘kmeans’
decom.initial: no visible global function definition for ‘quantile’
decom.initial: no visible global function definition for ‘var’
dispersion.nb.QL: no visible binding for global variable ‘quantile’
est.mu.nb.mle: no visible global function definition for ‘runif’
est.v.nb.QL: no visible global function definition for ‘runif’
pdf2grid: no visible global function definition for ‘dnorm’
pdf2grid: no visible global function definition for ‘dgamma’
prior.grid: no visible global function definition for ‘sd’
prior.grid: no visible global function definition for ‘dnorm’
test.AMAP: no visible global function definition for ‘rgamma’
test.AMAP: no visible global function definition for ‘rnorm’
test.AMAP: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Rd file 'MGN.EM.Rd':
  \usage lines wider than 90 characters:
     MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)

Rd file 'test.AMAP.Rd':
  \usage lines wider than 90 characters:
     test.AMAP(data, MGN, del.lim = NULL, FC = NULL, print.steps = FALSE, Integration = "MC",nMC=NULL)
  \examples lines wider than 100 characters:
     data("SimuHapMap")  # a matrix 'counts' storing simulated data with 10000 genes, two treatments, of which each has 5 replicates

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Zelig’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
amltest: no visible global function definition for ‘var’
amltest: no visible global function definition for ‘optim’
amltest: no visible global function definition for ‘lm’
cleanclust: no visible global function definition for ‘cor’
cleanclust: no visible global function definition for ‘hclust’
cleanclust: no visible global function definition for ‘as.dist’
cleanclust: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘SparkR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Analyz.loadSteps,Analyz: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for ‘plot.new’
andrews: no visible global function definition for ‘plot.window’
andrews: no visible global function definition for ‘title’
andrews: no visible global function definition for ‘axis’
andrews: no visible global function definition for ‘box’
andrews: no visible global function definition for ‘lines’
andrews: no visible global function definition for ‘rainbow’
andrews: no visible global function definition for ‘hsv’
selectand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tmg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
aw_map: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘boot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for ‘boot’
Undefined global functions or variables:
  boot
Packages in Depends field not imported from:
  ‘boot’ ‘lme4’
  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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘apollo/R/apollo_attach.R’:
  attach(as.list(apollo_beta), warn.conflicts = FALSE)
  attach(database, warn.conflicts = FALSE)
  attach(draws, warn.conflicts = FALSE)
  attach(randcoeff, warn.conflicts = FALSE)
  attach(lcpars, warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of ‘nline’ to
  ‘nlines’
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for ‘filter’
ardec.lm: no visible global function definition for ‘ar’
ardec.lm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'sdafilter.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

Rd file 'vmask.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/artfima.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘ARTP’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MSToutput.txt’
ASP.Score: no visible global function definition for ‘pnorm’
Graphs.Bayesian: no visible global function definition for ‘dev.new’
colorhex: no visible global function definition for ‘gray’
colorhex: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for ‘dbinom’
CALPHA: no visible global function definition for ‘pchisq’
CAST: no visible global function definition for ‘fisher.test’
CAST: no visible global function definition for ‘chisq.test’
CMC: no visible global function definition for ‘pf’
MULTI: no visible global function definition for ‘complete.cases’
RVT1: no visible global function definition for ‘pchisq’
RVT2: no visible global function definition for ‘pchisq’
RWAS: no visible global function definition for ‘pnorm’
SKAT: no visible global function definition for ‘dbeta’
SKAT: no visible global function definition for ‘pchisq’
TTEST: no visible global function definition for ‘complete.cases’
TTEST: no visible global function definition for ‘pf’
WST: no visible global function definition for ‘mvfft’
WST: no visible global function definition for ‘pnorm’
my_cmc_method: no visible global function definition for
  ‘complete.cases’
my_getUV: no visible global function definition for ‘complete.cases’
my_orwss_method: no visible global function definition for ‘sd’
my_rarecov_method: no visible global function definition for
  ‘chisq.test’
my_rbt_method: no visible global function definition for ‘ppois’
my_score_method: no visible global function definition for ‘pchisq’
my_ssu_method: no visible global function definition for ‘pchisq’
my_ssuw_method: no visible global function definition for ‘pchisq’
my_sum_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pmvnorm’
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘asteRiskData’
GNU make is a SystemRequirements.
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par pnorm points printCoefmat qnorm tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf png quantile rnorm runif sd
  var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
PlotAtm.lin : scale_image: no visible global function definition for
  ‘heat.colors’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘par’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘sd’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘approx’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘image’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘axis’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘mtext’
PlotAtm.lin: no visible global function definition for ‘arrows’
PlotAtm.lin: no visible global function definition for ‘text’
PlotAtm.lin: no visible global function definition for ‘polygon’
sky.colors: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Rd file 'MakeArrivals.lin.Rd':
  \examples lines wider than 100 characters:
     MakeArrivals.lin(xs = c(100, 150), ys = c(100, 150), zs = c(100, 150), xr = 0, yr = 0, zr = 0, dt = 0.01, nt = 100, timing = c(0, 0), A ... [TRUNCATED]

Rd file 'MakeAtmList.lin.Rd':
  \usage lines wider than 90 characters:
     MakeAtmList.lin(z0 = 0, c0 = 343, gc = 0, wx0 = 0, gwx = 0, wy0 = 0, gwy = 0, rho0 = 1.2929 * exp(-z0/6800), grho = -0.0001901323 * exp ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
plot.AUC: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines
Consider adding
  importFrom("graphics", "lines")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for ‘predict’
plot.AUCRF: no visible global function definition for ‘par’
plot.AUCRF: no visible global function definition for ‘dotchart’
plot.AUCRF: no visible global function definition for ‘title’
plot.AUCRF: no visible global function definition for ‘text’
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘RJSONIO’ ‘hexbin’ ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for ‘hist’
audioHist: no visible global function definition for ‘rescale’
audioHist: no visible global function definition for ‘toJSON’
audioScatter: no visible binding for global variable ‘formula’
audioScatter: no visible global function definition for ‘hexbinplot’
audioScatter: no visible global function definition for ‘cor’
audioScatter: no visible global function definition for ‘toJSON’
audioSplom: no visible global function definition for ‘hexplom’
audioSplom: no visible binding for global variable ‘BTY’
audioSplom: no visible binding for global variable ‘panel.hexboxplot’
audioSplom: no visible global function definition for ‘combn’
audioSplom : <anonymous>: no visible global function definition for
  ‘cor’
audioSplom : <anonymous>: no visible global function definition for
  ‘toJSON’
audiolyzRcheck: no visible global function definition for
  ‘download.file’
audiolyzRcheck: no visible global function definition for ‘unzip’
matricize: no visible global function definition for ‘hexbin’
panel.audiolyzR: no visible global function definition for
  ‘panel.hexbinplot’
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls in package code:
  ‘ggplot2’ ‘gpclib’ ‘maptools’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gLog.ep: no visible global function definition for ‘quantile’
gedestp: no visible global function definition for ‘na.omit’
gedestp: no visible global function definition for ‘optim’
gets.mean: no visible global function definition for ‘start’
gets.mean: no visible global function definition for ‘end’
gets.mean: no visible global function definition for ‘window’
gets.mean: no visible global function definition for ‘pt’
gets.mean: no visible global function definition for ‘Box.test’
gets.mean: no visible global function definition for ‘pchisq’
gets.vol: no visible global function definition for ‘start’
gets.vol: no visible global function definition for ‘end’
gets.vol: no visible global function definition for ‘window’
gets.vol: no visible global function definition for ‘pt’
gets.vol: no visible global function definition for ‘Box.test’
gets.vol: no visible global function definition for ‘pchisq’
jb.test: no visible global function definition for ‘pchisq’
skewness.test: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘start’
sm: no visible global function definition for ‘end’
sm: no visible global function definition for ‘window’
sm: no visible global function definition for ‘pt’
sm: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘Box.test’
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
CRexp_set: no visible global function definition for ‘runif’
b6e6rl: no visible global function definition for ‘runif’
derand_RL: no visible global function definition for ‘runif’
derandexp_RL: no visible global function definition for ‘runif’
nahvyb_expt: no visible global function definition for ‘runif’
roulete: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for ‘sd’
.generateUnitHyperCube: no visible global function definition for
  ‘runif’
.makeBoundedSingleStep: no visible global function definition for
  ‘runif’
.makeBoundedStep: no visible global function definition for ‘runif’
.makeStep: no visible global function definition for ‘runif’
.staircaseSampling: no visible global function definition for ‘runif’
GaussianPrior: no visible global function definition for ‘qnorm’
LogNormalPrior: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail vcov
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
‘library’ or ‘require’ call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
best_binomial_bandit : f: no visible global function definition for
  ‘dbeta’
best_binomial_bandit : f: no visible global function definition for
  ‘pbeta’
best_binomial_bandit: no visible global function definition for
  ‘integrate’
best_poisson_bandit : f: no visible global function definition for
  ‘dgamma’
best_poisson_bandit : f: no visible global function definition for
  ‘pgamma’
best_poisson_bandit: no visible global function definition for
  ‘integrate’
deseasonalized_trend: no visible global function definition for
  ‘predict’
distribution_estimate: no visible global function definition for
  ‘quantile’
distribution_estimate: no visible global function definition for
  ‘qbeta’
significance_analysis: no visible global function definition for
  ‘prop.test’
sim_post: no visible global function definition for ‘rbeta’
summarize_metrics: no visible global function definition for ‘median’
summarize_metrics: no visible global function definition for
  ‘prop.test’
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘grid’ ‘lattice’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for ‘unit’
barcode: no visible global function definition for ‘grid.newpage’
barcode: no visible global function definition for ‘grid.text’
barcode: no visible global function definition for ‘gpar’
barcode: no visible global function definition for ‘pushViewport’
barcode: no visible global function definition for ‘viewport’
barcode: no visible global function definition for ‘convertHeight’
barcode: no visible global function definition for ‘convertWidth’
barcode: no visible global function definition for ‘grid.rect’
barcode: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for ‘unit’
barcode.panel: no visible global function definition for ‘hist’
barcode.panel: no visible global function definition for ‘pushViewport’
barcode.panel: no visible global function definition for ‘viewport’
barcode.panel: no visible global function definition for ‘grid.xaxis’
barcode.panel: no visible global function definition for ‘gpar’
barcode.panel: no visible global function definition for ‘grid.text’
barcode.panel: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for
  ‘grid.segments’
barcode.panel: no visible global function definition for ‘grid.points’
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
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.
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
FECRT: no visible global function definition for ‘pdf’
FECRT: no visible global function definition for ‘hist’
FECRT: no visible global function definition for ‘abline’
FECRT: no visible global function definition for ‘dev.off’
FECRT.analysis: no visible global function definition for ‘pdf’
FECRT.analysis: no visible global function definition for ‘hist’
FECRT.analysis: no visible global function definition for ‘abline’
FECRT.analysis: no visible global function definition for ‘dev.off’
fecrt: no visible global function definition for ‘pdf’
fecrt: no visible global function definition for ‘hist’
fecrt: no visible global function definition for ‘abline’
fecrt: no visible global function definition for ‘dev.off’
fecrt.analysis: no visible global function definition for ‘pdf’
fecrt.analysis: no visible global function definition for ‘hist’
fecrt.analysis: no visible global function definition for ‘abline’
fecrt.analysis: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
BMAnimalTrack: no visible global function definition for ‘nlm’
BMAnimalTrack: no visible global function definition for ‘qnorm’
dataSim: no visible global function definition for ‘rnorm’
rBBridge: no visible global function definition for ‘rnorm’
rBMotion: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
noninform_prior : a : f1: no visible global function definition for
  ‘pbeta’
noninform_prior : a : f1: no visible global function definition for
  ‘dbeta’
noninform_prior : a: no visible global function definition for
  ‘integrate’
noninform_prior: no visible global function definition for ‘rbeta’
noninform_prior: no visible global function definition for ‘optim’
postNullFun : b : f1: no visible global function definition for ‘pbeta’
postNullFun : b : f1: no visible global function definition for ‘dbeta’
postNullFun : b: no visible global function definition for ‘integrate’
prior_prob : a : f1: no visible global function definition for ‘pbeta’
prior_prob : a : f1: no visible global function definition for ‘dbeta’
prior_prob : a: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘gplots’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
‘library’ or ‘require’ call to ‘coda’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'BPSpostSample.Rd':
  \usage lines wider than 90 characters:
     BPSpostSample(hyp, times, obs = NULL, mclen = 10, burnin = 0, thin = 1, df = 10, etastar = NULL)
  \examples lines wider than 100 characters:
     post<-BPSpostSample(hypars, times = earthquakes$ti, obs = earthquakes$ob, etastar = postmode$etastar)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘diagnostics.pdf’ ‘post.rda’
Packages in Depends field not imported from:
  ‘fields’ ‘poibin’ ‘rjags’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for ‘heat.colors’
BMR.plot: no visible global function definition for ‘image.plot’
BMR.plot: no visible global function definition for ‘title’
BMR.plot: no visible global function definition for ‘mtext’
BMR.plot: no visible global function definition for ‘par’
baysic.data: no visible global function definition for ‘layout’
baysic.data: no visible global function definition for ‘barplot’
baysic.data: no visible global function definition for ‘rainbow’
baysic.fit: no visible global function definition for ‘jags.model’
baysic.fit: no visible global function definition for ‘update’
baysic.fit: no visible global function definition for ‘coda.samples’
baysic.test: no visible global function definition for ‘ppois’
baysic.test : <anonymous>: no visible global function definition for
  ‘ppoibin’
baysic.test: no visible global function definition for ‘pbinom’
fuzzy.FDR.approx: no visible global function definition for ‘p.adjust’
fuzzy.FDR.approx: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
Rd file 'baysic.fit.Rd':
  \usage lines wider than 90 characters:
     baysic.fit(dat.out, snv.cat, covar = NULL, excl.list = NULL, burn.in = 10000,n.samp = 25000, fn.jags = "baysic.jags", prior = NULL)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

Rd file 'baysic.test.Rd':
  \usage lines wider than 90 characters:
     baysic.test(dat.out, fit.out, fdr.level = 0.15, fuzzy.cnt = 10000, r = NULL,subtype = NULL, PB.approx = FALSE)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

These lines will be truncated in the PDF manual.
BAYSTAR: no visible global function definition for ‘median’
BAYSTAR: no visible global function definition for ‘ar’
BAYSTAR: no visible global function definition for ‘quantile’
BAYSTAR: no visible global function definition for ‘dev.new’
BAYSTAR: no visible global function definition for ‘ts.plot’
BAYSTAR: no visible global function definition for ‘title’
BAYSTAR: no visible global function definition for ‘par’
BAYSTAR: no visible global function definition for ‘plot.ts’
BAYSTAR: no visible global function definition for ‘lines’
BAYSTAR: no visible global function definition for ‘acf’
TAR.lagd: no visible global function definition for ‘runif’
TAR.sigma: no visible global function definition for ‘rgamma’
TAR.simu: no visible global function definition for ‘rnorm’
TAR.summary: no visible global function definition for ‘quantile’
TAR.summary: no visible global function definition for ‘sd’
TAR.thres: no visible global function definition for ‘rnorm’
TAR.thres: no visible global function definition for ‘runif’
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
LaplaceMetropolis_admkr: no visible binding for global variable
  ‘median’
LaplaceMetropolis_admkr: no visible global function definition for
  ‘mad’
LaplaceMetropolis_gaussian: no visible binding for global variable
  ‘median’
LaplaceMetropolis_gaussian: no visible global function definition for
  ‘mad’
cost_admkr: no visible global function definition for ‘sd’
cov_chol: no visible global function definition for ‘qchisq’
cov_chol_admkr: no visible global function definition for ‘qchisq’
gibbs_admkr_erro: no visible global function definition for ‘rnorm’
gibbs_admkr_erro: no visible global function definition for ‘runif’
gibbs_admkr_nw: no visible global function definition for ‘qnorm’
gibbs_admkr_nw: no visible global function definition for ‘rnorm’
gibbs_admkr_nw: no visible global function definition for ‘runif’
loglikelihood_admkr: no visible global function definition for ‘sd’
margin_like_admkr: no visible global function definition for ‘sd’
np_gibbs: no visible global function definition for ‘qnorm’
np_gibbs: no visible global function definition for ‘rnorm’
np_gibbs: no visible global function definition for ‘runif’
np_gibbs: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
bbmm.contour: no visible global function definition for ‘na.omit’
bbmm.contour: no visible global function definition for ‘optimize’
bbmm.contour: no visible global function definition for ‘contour’
bbmm.contour: no visible global function definition for ‘points’
bbmm.contour: no visible global function definition for ‘lines’
brownian.bridge: no visible global function definition for ‘sd’
brownian.motion.variance: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
Undefined global functions or variables:
  runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignette.Rmd’
pairs.bce : panel.cor: no visible global function definition for ‘text’
pairs.bce : panel.cor: no visible global function definition for ‘cor’
pairs.bce : panel.hist: no visible global function definition for ‘par’
pairs.bce : panel.hist: no visible global function definition for
  ‘hist’
pairs.bce : panel.hist: no visible global function definition for
  ‘rect’
pairs.bce: no visible global function definition for ‘pairs’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
rdirichlet2: no visible global function definition for ‘rgamma’
summary.bce: no visible global function definition for ‘cov’
summary.bce: no visible binding for global variable ‘sd’
summary.bce: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bcpmeta.model: no visible global function definition for ‘rbinom’
bcpmeta.model: no visible global function definition for ‘runif’
bcpmeta.parameters: no visible global function definition for ‘runif’
cp.plot: no visible global function definition for ‘postscript’
cp.plot: no visible global function definition for ‘lines’
cp.plot: no visible global function definition for ‘axis’
cp.plot: no visible global function definition for ‘box’
cp.plot: no visible global function definition for ‘points’
cp.plot: no visible global function definition for ‘dev.off’
lMarLik.EB.normAR: no visible global function definition for ‘optimize’
lMarLik.normAR: no visible global function definition for ‘integrate’
marginal.plot: no visible global function definition for ‘postscript’
marginal.plot: no visible global function definition for ‘axis’
marginal.plot: no visible global function definition for ‘box’
marginal.plot: no visible global function definition for ‘points’
marginal.plot: no visible global function definition for ‘dev.off’
simgen: no visible global function definition for ‘rnorm’
up.eta.MH.normAR: no visible global function definition for ‘runif’
up.eta.RS.normAR: no visible global function definition for ‘runif’
up.parameters.EB.normAR: no visible global function definition for
  ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘runif’
up.parameters.normAR: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  axis box dev.off integrate lines optimize points postscript rbinom
  rgamma rnorm runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "box", "lines", "points")
  importFrom("stats", "integrate", "optimize", "rbinom", "rgamma",
             "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
mise: no visible global function definition for ‘integrate’
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for ‘dbeta’
density,Chen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,Vitale : <anonymous>: no visible global function definition for
  ‘dbeta’
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for ‘integrate’
distribution,KernelDensity : <anonymous>: no visible global function
  definition for ‘integrate’
print,BoundedDensity: no visible global function definition for ‘str’
print,KernelDensity: no visible global function definition for ‘str’
rsample,BoundedDensity: no visible global function definition for
  ‘runif’
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for ‘integrate’
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  ‘dbeta’
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for ‘integrate’
show,BoundedDensity: no visible global function definition for ‘str’
show,KernelDensity: no visible global function definition for ‘str’
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘bferrbars.eps’ ‘dataplot.eps’ ‘ppdat.eps’ ‘ppmod.eps’
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘beadarray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for ‘na.omit’
beadtypeFilter: no visible global function definition for ‘exprs’
beadtypeFilter: no visible global function definition for ‘se.exprs’
beadtypeFilter: no visible global function definition for ‘beadNum’
beadtypeFilter: no visible global function definition for ‘fData’
emCDF: no visible global function definition for ‘brewer.pal’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Rd file 'iccFun.Rd':
  \examples lines wider than 100 characters:
     aaa<-na.omit(data.frame(I(rownames(exprs(exampleSummaryDataNorm))),exprs(exampleSummaryDataNorm)))[1:40,]

These lines will be truncated in the PDF manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/beanz.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/beast.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘example_Initial.parameters.Robj’ ‘example_MCMC_output1.Robj’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
block.gibbs: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for ‘par’
global: no visible global function definition for ‘runif’
global: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘par’
mymcmc: no visible global function definition for ‘rnorm’
mymcmc: no visible global function definition for ‘runif’
mymcmc: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘lines’
plkhci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘betareg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for ‘predict’
bias: no visible global function definition for ‘pnorm’
bias: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘svyPVpack’
Package suggested but not available for checking: ‘INLA’
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
GNU make is a SystemRequirements.
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outputs’
Malformed Description field: should contain one or more complete sentences.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for ‘chisq.test’
rmultnom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bin_ps: no visible global function definition for ‘runif’
bin_ps: no visible global function definition for ‘dbinom’
draw_i: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  ‘flush.console’
dRUMAuxMix: no visible global function definition for ‘flush.console’
dRUMHAM: no visible global function definition for ‘flush.console’
dRUMIndMH: no visible global function definition for ‘flush.console’
print.binomlogit: no visible global function definition for ‘is’
summary.binomlogit: no visible global function definition for ‘is’
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
‘library’ or ‘require’ calls in package code:
  ‘ggplot2’ ‘lattice’ ‘polynom’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
bins.quantiles: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘lmfor’ in Rd xrefs
Package which this enhances but not available for checking: ‘asreml’
‘library’ or ‘require’ call to ‘MGRASTer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
biom.matrix: no visible global function definition for ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
biwt.cor: no visible global function definition for ‘covMcd’
biwt.cor: no visible binding for global variable ‘mad’
biwt.est: no visible global function definition for ‘covMcd’
biwt.est: no visible global function definition for ‘mahalanobis’
chi.int: no visible global function definition for ‘pchisq’
chi.int.p: no visible global function definition for ‘dchisq’
chi.int2: no visible global function definition for ‘pchisq’
chi.int2.p: no visible global function definition for ‘dchisq’
rejpt.bw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
blockMessage : <anonymous>: no visible global function definition for
  ‘head’
blockMessage: no visible global function definition for ‘head’
blockMessage: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘coda’ ‘functional’ ‘plyr’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘coda’ ‘functional’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for ‘density’
HDistSize: no visible global function definition for ‘density’
bmkconverge: no visible global function definition for ‘Compose’
bmksensitive: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Curry’
bmksummary: no visible binding for global variable ‘quantile’
bmksummary : std.error: no visible global function definition for ‘var’
bmksummary: no visible global function definition for ‘mcmc’
bmksummary: no visible global function definition for ‘mcmc.list’
bmksummary: no visible global function definition for ‘median’
bmksummary: no visible global function definition for ‘effectiveSize’
bmksummary: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
bmmix : LL.y: no visible global function definition for ‘dmultinom’
bmmix : LL.x : <anonymous>: no visible global function definition for
  ‘dmultinom’
bmmix : LPrior.alpha: no visible global function definition for ‘dexp’
bmmix : alpha.move: no visible global function definition for ‘rnorm’
bmmix : alpha.move: no visible global function definition for ‘runif’
bmmix : phi.move: no visible global function definition for ‘rnorm’
bmmix : phi.move: no visible global function definition for ‘runif’
bmmix: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘mcmc.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
make_topology: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bnlr: no visible global function definition for ‘dnorm’
bnlr: no visible global function definition for ‘runif’
chainsum : <anonymous>: no visible global function definition for
  ‘quantile’
infocrit: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BOGest: no visible global function definition for ‘read.table’
BOGstat: no visible global function definition for ‘phyper’
BOGstat: no visible global function definition for ‘wilcox.test’
BOGstat: no visible global function definition for ‘p.adjust’
gseaplot: no visible global function definition for ‘par’
gseaplot: no visible global function definition for ‘points’
gseaplot: no visible global function definition for ‘axis’
gseaplot: no visible global function definition for ‘segments’
hgplot: no visible global function definition for ‘par’
hgplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  axis barplot p.adjust par phyper points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "points", "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘attractors.tex’ ‘cellcycle.sbml’ ‘cellcycle.txt’ ‘pajek_export.net’
  ‘sequence.txt’ ‘testNet.bn’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
specdens: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'specdens.Rd':
  \examples lines wider than 100 characters:
                                                                                         #the first 20 values of the 
                                                                                         #time series Nile and WWWusage

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
boottol: no visible global function definition for ‘setNames’
boottol : shift: no visible global function definition for ‘tail’
boottol : shift: no visible global function definition for ‘head’
boottol: no visible global function definition for ‘na.omit’
vastol: no visible global function definition for ‘setNames’
vastol: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'beq.lin.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol0,type="l",lty=1,main=paste("Water Surface Elevetion after",t,"days",sep=" "),xlab="x[m]",ylab="h[m]")

Rd file 'beq.song.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol1,type="l",lty=1,main="Water Surface Elevetion (Song at's solution) ",xlab="x[m]",ylab="h[m]")

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
bPeaksAnalysis: no visible global function definition for ‘write.table’
dataReading: no visible global function definition for ‘read.table’
dataSmoothing: no visible global function definition for ‘filter’
peakDetection: no visible global function definition for ‘quantile’
peakDetection: no visible global function definition for ‘pdf’
peakDetection: no visible global function definition for ‘par’
peakDetection: no visible global function definition for ‘text’
peakDetection: no visible global function definition for ‘abline’
peakDetection: no visible global function definition for ‘points’
peakDetection: no visible global function definition for ‘dev.off’
peakDetection: no visible global function definition for ‘write.table’
peakDrawing: no visible global function definition for ‘par’
peakDrawing: no visible global function definition for ‘abline’
peakLocation: no visible global function definition for ‘read.table’
peakLocation: no visible global function definition for ‘pdf’
peakLocation: no visible global function definition for ‘barplot’
peakLocation: no visible global function definition for ‘dev.off’
peakLocation: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline barplot dev.off filter par pdf points quantile read.table text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘bPeaks_example-chrIV.bed’ ‘bPeaks_example-chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example-chrIV_dataSummary.pdf’
  ‘bPeaks_example_bPeaks_allGenome.bed’
  ‘bPeaks_example_bPeaks_parameterSummary.txt’
  ‘bPeaks_example_chrIV.bed’ ‘bPeaks_example_chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example_chrIV_dataSummary.pdf’
  ‘bPeaks_example_peakLocation.pdf’
  ‘bPeaks_example_peakLocation_inCDS.txt’
  ‘bPeaks_example_peakLocation_inPromoters.txt’ ‘peakStats.Robject’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim points text
Consider adding
  importFrom("graphics", "abline", "contour", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
Running examples in ‘broom.mixed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glmmTMB_tidiers
> ### Title: Tidying methods for glmmTMB models
> ### Aliases: glmmTMB_tidiers tidy.glmmTMB augment.glmmTMB glance.glmmTMB
> 
> ### ** Examples
> 
> if (require("glmmTMB") && require("lme4")) {
+     data("sleepstudy",package="lme4")
+     ## original model:
+     ## Not run: 
+ ##D         lmm1 <- glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
+ ##D     
+ ## End(Not run)
+     ## load stored object
+     load(system.file("extdata","glmmTMB_example.rda",package="broom.mixed"))
+     tidy(lmm1)
+     tidy(lmm1, effects = "fixed")
+     tidy(lmm1, effects = "fixed", conf.int=TRUE)
+     tidy(lmm1, effects = "fixed", conf.int=TRUE, conf.method="uniroot")
+     ## FIX: tidy(lmm1, effects = "ran_vals", conf.int=TRUE)
+     head(augment(lmm1, sleepstudy))
+     glance(lmm1)
+ 
+     ## original model:
+     ##  glmm1 <- glmmTMB(incidence/size ~ period + (1 | herd),
+     ##                  data = cbpp, family = binomial, weights=size)
+     tidy(glmm1)
+     tidy(glmm1, effects = "fixed")
+     tidy(glmm1, effects = "fixed", exponentiate=TRUE)
+     tidy(glmm1, effects = "fixed", conf.int=TRUE, exponentiate=TRUE)
+     head(augment(glmm1, cbpp))
+     head(augment(glmm1, cbpp, type.residuals="pearson"))
+     glance(glmm1)
+ ## Not run: 
+ ##D     ## profile CIs - a little bit slower but more accurate
+ ##D     tidy(glmm1, effects = "fixed", conf.int=TRUE, exponentiate=TRUE, conf.method="profile")
+ ## End(Not run)
+ }
Loading required package: glmmTMB
Loading required package: lme4
Loading required package: Matrix
Error in .Call("MakeDoubleFunObject", data, parameters, reportenv, PACKAGE = DLL) : 
  Incorrect number of arguments (3), expecting 4 for 'MakeDoubleFunObject'
Calls: tidy ... VarCorr -> VarCorr.glmmTMB -> <Anonymous> -> f -> retape
Execution halted
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
BSGS.Sample: no visible global function definition for ‘rgamma’
BSGS.Simple: no visible global function definition for ‘rgamma’
CompWiseGibbs: no visible global function definition for ‘runif’
CompWiseGibbs: no visible global function definition for ‘rnorm’
CompWiseGibbsSMP: no visible global function definition for ‘rbinom’
CompWiseGibbsSMP: no visible global function definition for ‘runif’
CompWiseGibbsSMP: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘runif’
CompWiseGibbsSimple: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘rgamma’
GroupMH: no visible global function definition for ‘runif’
GroupZ.MH: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
plot.bspec: no visible global function definition for ‘par’
plot.bspec: no visible global function definition for ‘matlines’
plot.bspec: no visible global function definition for ‘points’
plot.bspec: no visible global function definition for ‘axis’
plot.bspec: no visible global function definition for ‘mtext’
plot.bspec: no visible global function definition for ‘axTicks’
plot.bspec: no visible global function definition for ‘box’
plot.bspecACF: no visible global function definition for ‘abline’
plot.bspecACF: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "points")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
alpha.proxy: no visible global function definition for ‘filled.contour’
alpha.proxy: no visible global function definition for ‘axis’
alpha.proxy: no visible global function definition for ‘contour’
factor.model.stat: no visible global function definition for ‘quantile’
factor.model.stat: no visible global function definition for ‘lsfit’
partial.rainbow: no visible binding for global variable ‘rainbow’
var.shrink.eqcor: no visible global function definition for ‘var’
var.shrink.eqcor: no visible global function definition for ‘quantile’
var.shrink.eqcor: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'bvenn.Rd':
  \examples lines wider than 100 characters:
                     bvenn(list(Set1 = sample(letters, 16), Set2 = sample(letters, 3+ 3*j), Set3 = sample(letters, 7)), add = TRUE, fontsize ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
makemim: no visible global function definition for ‘cor’
sigtestMTC: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bootstrapCapwire: no visible global function definition for ‘quantile’
drawCapRatesBeta : <anonymous>: no visible global function definition
  for ‘rbeta’
drawCapRatesExp : <anonymous>: no visible global function definition
  for ‘rexp’
drawCapRatesGamma : <anonymous>: no visible global function definition
  for ‘rgamma’
drawCapRatesGeom : <anonymous>: no visible global function definition
  for ‘rgeom’
drawCapRatesUnif : <anonymous>: no visible global function definition
  for ‘runif’
partitionCountData : find.3.way.partitions: no visible global function
  definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for ‘qnorm’
as.record: no visible global function definition for ‘capture.output’
estN: no visible global function definition for ‘sd’
estN: no visible global function definition for ‘qnorm’
estN.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
abundance: no visible global function definition for ‘D’
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for ‘barplot’
barplotEQR: no visible global function definition for ‘abline’
barplotEQR: no visible global function definition for ‘par’
barplotEQR: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘foo.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘Vignette.Rmd’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘cartools.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
'LazyData' is specified without a 'data' directory
MDR.high.forward1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for
  ‘complete.cases’
MDR.sing.mod1: no visible global function definition for ‘lm’
MDR.sing.mod1: no visible global function definition for ‘aov’
MDR.sing.mod1: no visible global function definition for ‘anova’
MDR.stage.forward1: no visible global function definition for ‘combn’
MDR.stage.forward1: no visible global function definition for
  ‘complete.cases’
MDR.stage.forward1: no visible global function definition for ‘lm’
MDR.stage.forward1: no visible global function definition for ‘resid’
MDR.stage.forward1: no visible global function definition for ‘pf’
MDR_forward1: no visible global function definition for
  ‘complete.cases’
MDR_forward1: no visible global function definition for ‘lm’
MDR_forward1: no visible global function definition for ‘aov’
low.anova: no visible global function definition for ‘complete.cases’
low.anova: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘combn’
sing.mod1: no visible global function definition for ‘complete.cases’
sing.mod1: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for ‘xtabs’
mob.eqmain: no visible global function definition for ‘model.matrix’
mob.qi: no visible global function definition for ‘C’
mob.qi: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘C’
mob.rc1: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘model.matrix’
mob.symint: no visible global function definition for ‘model.matrix’
print.ctab: no visible global function definition for ‘ftable’
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
Rd file 'ctab.Rd':
  \usage lines wider than 90 characters:
     ctab(...,dec.places=NULL,digits=NULL,type=NULL,style=NULL,row.vars=NULL,col.vars=NULL,percentages=NULL,addmargins=NULL)

Rd file 'sqtab.Rd':
  \examples lines wider than 100 characters:
     OccFather<-gl(5,5,labels=c("Upper nonmanual","Lower nonmanual","Upper manual","Lower manual","Farm"))
     glm.q0<-glm(Freq~OccFather+OccSon+mob.qi(OccFather,OccSon,constrained=TRUE),family=poisson(),data=FHtab)
     glm.hrc1<-glm(Freq~OccFather+OccSon+mob.rc1(OccFather,OccSon,equal=TRUE),family=poisson(),data=FHtab)
     m2 <- mlogit(occupation ~ mob.qi(focc,alt)+mob.unif(focc,alt) | education+race,data=pc, reflevel = "farm")

These lines will be truncated in the PDF manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
ccd.sequential: no visible global function definition for ‘qchisq’
dominate.random.sample: no visible global function definition for
  ‘runif’
draw.circle: no visible global function definition for ‘polygon’
juggle2: no visible global function definition for ‘rbinom’
plot.cccd: no visible global function definition for ‘gray’
plot.cccd: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘points’
Undefined global functions or variables:
  gray points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
VD: no visible binding for global variable ‘var’
stratcc : <anonymous>: no visible global function definition for
  ‘hclust’
stratcc : <anonymous>: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
Rd file 'stratcc.Rd':
  \usage lines wider than 90 characters:
     stratcc(x, groups, alloc = "Pro", fraction = 0.1, clustering = FALSE, cluster_method = "ward")

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
p.Roy: no visible global function definition for ‘pf’
p.asym: no visible global function definition for ‘pf’
p.perm: no visible global function definition for ‘cancor’
plt.asym: no visible global function definition for ‘qf’
plt.asym: no visible global function definition for ‘df’
plt.asym: no visible global function definition for ‘abline’
plt.perm: no visible global function definition for ‘hist’
plt.perm: no visible global function definition for ‘mtext’
plt.perm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cancor df hist mtext pf qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
Rd file 'p.perm.Rd':
  \examples lines wider than 100 characters:
     ## Run permutation test using Wilks Lambda (default) as test statistic; include different numbers of canonical correlations:

Rd file 'plt.asym.Rd':
  \examples lines wider than 100 characters:
     ## Plot the F-approximation for the Hotelling-Lawley Trace, considering 3, 2, or 1 canonical correlation(s):

Rd file 'plt.perm.Rd':
  \examples lines wider than 100 characters:
     # plot the permutation distribution of an F approximation for Wilks' Lambda, considering 3 and 2 canonical correlations:
     # plot the permutation distribution of an F approximation for the Pillai-Bartlett Trace, considering 3, 2, and 1 canonical correlation( ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘bitops’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  ‘Base.txt’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘gplots’ ‘minpack.lm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for ‘pnorm’
fitVolDist: no visible global function definition for ‘nls.lm’
fitVolDist: no visible global function definition for ‘nls.lm.control’
fitVolDist: no visible global function definition for ‘optim’
fitVolDist: no visible global function definition for ‘relist’
print.fitVolDist: no visible global function definition for ‘coef’
print.fitVolDist: no visible global function definition for ‘deviance’
print.fitVolDist: no visible global function definition for ‘pt’
print.fitVolDist: no visible global function definition for
  ‘printCoefmat’
resFunChiSq: no visible global function definition for ‘relist’
volEq7: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/censorcopula.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for ‘dnorm’
MomNIT: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘lm’
em.cens: no visible global function definition for ‘coefficients’
em.cens : ft: no visible global function definition for ‘dt’
em.cens : ft: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘optimize’
em.cens: no visible global function definition for ‘dnorm’
em.cens: no visible global function definition for ‘pnorm’
em.cens: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cepp.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Hartree2Joule: no visible binding for global variable
  ‘universalConstants’
Hertz2Joule: no visible binding for global variable
  ‘universalConstants’
Joule2Hartree: no visible binding for global variable
  ‘universalConstants’
Joule2Hertz: no visible binding for global variable
  ‘universalConstants’
Joule2Kelvin: no visible binding for global variable
  ‘universalConstants’
Joule2centimeterMinusOne: no visible binding for global variable
  ‘universalConstants’
Joule2electronVolt: no visible binding for global variable
  ‘universalConstants’
Joule2kiloCaloriePerMole: no visible binding for global variable
  ‘universalConstants’
Joule2kiloJoulePerMole: no visible binding for global variable
  ‘universalConstants’
KMC: no visible global function definition for ‘runif’
Kelvin2Joule: no visible binding for global variable
  ‘universalConstants’
LandauZener: no visible binding for global variable
  ‘universalConstants’
LandauZenerProbability: no visible binding for global variable
  ‘universalConstants’
Marcus: no visible binding for global variable ‘universalConstants’
MarcusLevichJortner: no visible binding for global variable
  ‘universalConstants’
centimeterMinusOne2Joule: no visible binding for global variable
  ‘universalConstants’
electronVolt2Joule: no visible binding for global variable
  ‘universalConstants’
kiloCaloriePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
kiloJoulePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘bitops’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for ‘read.csv’
createInventory: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for
  ‘getURLContent’
downloadMaster: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for ‘write.csv’
getMissingScrape: no visible global function definition for ‘read.csv’
readLocalMaster: no visible global function definition for ‘read.csv’
readMonthlyCsv: no visible global function definition for ‘read.csv’
scrapeToCsv: no visible global function definition for ‘download.file’
writeData: no visible global function definition for ‘write.csv’
writeGhcn: no visible global function definition for ‘write.table’
writeInventory: no visible global function definition for ‘write.table’
writeMonthlyStations: no visible global function definition for
  ‘read.csv’
writeMonthlyStations: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Rd file 'chebR.Rd':
  \examples lines wider than 100 characters:
     return(list(coefs=rlist$xx[1:n],resids=rlist$bb[1:m],rank=rlist$rank,iter=rlist$iter,ocode=rlist$ocode))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘darts’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘investr’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(chemCal)
  > 
  > test_check("chemCal")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_compare_investr.R:4:1): (code run outside of `test_that()`) ─────
  <packageNotFoundError/error/condition>
  Error in `library(investr)`: there is no package called 'investr'
  Backtrace:
      ▆
   1. └─base::library(investr) at test_compare_investr.R:4:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘stepres00.txt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Package vignette with placeholder title ‘Vignette Title’:
  ‘childhoodmortality.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for ‘var’
Qh.times.dhyper: no visible global function definition for ‘pnorm’
Qh.times.dhyper: no visible global function definition for ‘dhyper’
TDiM: no visible global function definition for ‘sd’
choplump.default: no visible global function definition for
  ‘flush.console’
choplump.formula: no visible global function definition for ‘terms’
cm.compact: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
parse_counts: 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘CISE_vignette.Rmd’
cit.assignBcmst: no visible binding for global variable ‘citbcmst’
cit.assignBcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignBcmst: no visible global function definition for ‘prcomp’
cit.assignBcmst: no visible global function definition for ‘par’
cit.assignBcmst: no visible global function definition for ‘lines’
cit.assignBcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable ‘citccmst’
cit.assignCcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignCcmst : median.na: no visible global function definition for
  ‘median’
cit.assignCcmst: no visible global function definition for ‘prcomp’
cit.assignCcmst: no visible global function definition for ‘par’
cit.assignCcmst: no visible global function definition for ‘lines’
cit.assignCcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘desciption-ciuupi.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rggobi’
‘library’ or ‘require’ call to ‘rggobi’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  ‘runif’
knnf: no visible global function definition for ‘terms’
rescaler.default: no visible global function definition for ‘sd’
rescaler.default: no visible global function definition for ‘median’
rescaler.default: no visible global function definition for ‘mad’
simvar.numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
<argument>  e_i e_i = \cases \{ +1 &
                                     if $1\leq i\leq p$\cr -1 & if $p+1\leq ...
l.2060 }{}
          
! Display math should end with $$.
<to be read again> 
                   1
l.2060 }{}
          
! Missing $ inserted.
<inserted text> 
                $
l.2060 }{}
          
! Misplaced \cr.
<argument> ...cases \{ +1 & if $1\leq i\leq p$\cr 
                                                  -1 & if $p+1\leq i\leq p+q...
l.2060 }{}
          
! Misplaced alignment tab character &.
<argument> ...s \{ +1 & if $1\leq i\leq p$\cr -1 &
                                                   if $p+1\leq i\leq p+q$\cr...
l.2060 }{}
          
! Misplaced \cr.
<argument> ...$\cr -1 & if $p+1\leq i\leq p+q$\cr 
                                                  0 & if $i>p+q$.\cr \} 
l.2060 }{}
          
! Misplaced alignment tab character &.
<argument> ...r -1 & if $p+1\leq i\leq p+q$\cr 0 &
                                                   if $i>p+q$.\cr \} 
l.2060 }{}
          
! Misplaced \cr.
<argument> ...eq i\leq p+q$\cr 0 & if $i>p+q$.\cr 
                                                  \} 
l.2060 }{}
          
! LaTeX Error: Bad math environment delimiter.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...
Found the following files/directories:
  ‘clifford-manual.tex’
Package suggested but not available for checking: ‘scio’
clime: no visible global function definition for ‘cov’
cv.clime: no visible global function definition for ‘cov’
cv.clime: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gxe.cc: no visible global function definition for ‘qnorm’
gxe.coh: no visible global function definition for ‘qnorm’
utility.cc: no visible global function definition for ‘qnorm’
utility.coh: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘clusterhap_reports’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
braycurtis: no visible global function definition for ‘as.dist’
czekanowski: no visible global function definition for ‘as.dist’
findComplementaryIndices: no visible global function definition for
  ‘na.omit’
genSimilarityProfile: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘hclust’
simprof.plot : <local> : colorizer: no visible global function
  definition for ‘is.leaf’
simprof.plot: no visible global function definition for ‘rainbow’
simprof.plot: no visible global function definition for ‘dendrapply’
simprof.plot: no visible global function definition for ‘as.dendrogram’
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for ‘median’
CNclusterNcenter: no visible binding for global variable ‘var’
breakIntoGaps: no visible global function definition for ‘runif’
centerprob: no visible global function definition for ‘pnorm’
getz: no visible global function definition for ‘predict’
smad: no visible global function definition for ‘mad’
smedian: no visible global function definition for ‘median’
smedian.sample: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
coalescentMCMC: no visible global function definition for
  ‘packageVersion’
coalescentMCMC : getparams: no visible global function definition for
  ‘nlminb’
sim.coalescent: no visible global function definition for ‘segments’
sim.coalescent: no visible global function definition for ‘points’
Undefined global functions or variables:
  nlminb packageVersion points segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls in package code:
  ‘lars’ ‘randomForest’ ‘ridge’ ‘snowfall’ ‘tree’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
COBRA : COBRA.lars: no visible global function definition for ‘lars’
COBRA : COBRA.lars: no visible global function definition for
  ‘predict.lars’
COBRA : COBRA.tree: no visible global function definition for ‘tree’
COBRA : COBRA.tree: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.tree: no visible global function definition for ‘predict’
COBRA : COBRA.ridge: no visible global function definition for
  ‘linearRidge’
COBRA : COBRA.ridge: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.ridge: no visible global function definition for
  ‘predict’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘randomForest’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘predict’
COBRA: no visible global function definition for ‘sfInit’
COBRA: no visible global function definition for ‘sfLibrary’
COBRA: no visible global function definition for ‘sfExportAll’
COBRA: no visible global function definition for ‘sfSapply’
COBRA: no visible global function definition for ‘sfStop’
COBRA: no visible global function definition for ‘write.table’
COBRA: no visible global function definition for ‘pdf’
COBRA: no visible global function definition for ‘points’
COBRA: no visible global function definition for ‘legend’
COBRA: no visible global function definition for ‘abline’
COBRA: no visible global function definition for ‘lines’
COBRA: no visible global function definition for ‘dev.off’
COBRA: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline as.formula dev.new dev.off lars legend linearRidge lines pdf
  points predict predict.lars randomForest sfExportAll sfInit sfLibrary
  sfSapply sfStop tree write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "points")
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Package in Depends field not imported from: ‘coda’
  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: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Rd file 'fast.flexsim.Rd':
  \usage lines wider than 90 characters:
     fast.flexsim(scale = 2, island,dispersalscale = 51, allee = 1, T = 1000, initp,parcombination, spnum = 2, sourcetype = "constant", type ... [TRUNCATED]

Rd file 'flexsim.Rd':
  \usage lines wider than 90 characters:
     flexsim(scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, initp,spnum = 2, island=10, sourcetype = "constant", type, path =  ... [TRUNCATED]

Rd file 'make.heatmap.Rd':
  \usage lines wider than 90 characters:
     make.heatmap(mat, type = "gray", xname = "x", yname = "y", xlab = NULL, ylab = NULL, title = NULL)

Rd file 'sim.coarse.Rd':
  \usage lines wider than 90 characters:
     sim.coarse(island=10,scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, type, initp, path = NULL)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BMDE: no visible global function definition for ‘quantile’
BMDU: no visible global function definition for ‘runif’
BMDU: no visible global function definition for ‘quantile’
FS: no visible global function definition for ‘qnorm’
GM: no visible global function definition for ‘qchisq’
QH: no visible global function definition for ‘qchisq’
SG : sgp: no visible global function definition for ‘ppois’
SG : sgp: no visible global function definition for ‘dpois’
WALD: no visible global function definition for ‘qchisq’
WALDCC: no visible global function definition for ‘qchisq’
WS: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘collectArgs_and_iterateWithArgs.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
cICA: no visible global function definition for ‘mvfft’
cICA: no visible global function definition for ‘ar.yw’
cICA: no visible global function definition for ‘rnorm’
scICA: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.text’
plotVenn2d: no visible global function definition for ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.text’
plotVenn3d: no visible global function definition for ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.polygon’
plotVenn4d : getCommonEllipse: no visible global function definition
  for ‘aggregate’
plotVenn4d : region.polygon: no visible global function definition for
  ‘head’
plotVenn4d : region.polygon: no visible global function definition for
  ‘grid.polygon’
plotVenn4d : region.polygon: no visible global function definition for
  ‘gpar’
plotVenn4d: no visible global function definition for ‘grid.text’
plotVenn4d: no visible global function definition for ‘gpar’
plotVenn4d: no visible global function definition for ‘pushViewport’
plotVenn4d: no visible global function definition for ‘viewport’
plotVenn4d: no visible global function definition for ‘grid.polygon’
plotVenn4d: no visible global function definition for ‘upViewport’
resizeCircles: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
generateMonochromaticColors: no visible global function definition for
  ‘col2rgb’
generateMonochromaticColors: no visible global function definition for
  ‘rgb’
generateMonochromaticColors: no visible global function definition for
  ‘tail’
hsv2rgb: no visible global function definition for ‘rgb’
rotational_dispersion: no visible global function definition for
  ‘col2rgb’
rotational_dispersion: no visible global function definition for
  ‘rgb2hsv’
tetradicColors: no visible global function definition for ‘head’
triadicColors: no visible global function definition for ‘head’
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for ‘rgb’
rgb.tables: no visible global function definition for ‘rgb’
ygobb: no visible global function definition for ‘approx’
ygobb: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘colr.Rmd’
Malformed Description field: should contain one or more complete sentences.
competitive.test: no visible global function definition for ‘runif’
selfcontained.test : fun2: no visible global function definition for
  ‘qchisq’
selfcontained.test: no visible global function definition for ‘cov’
selfcontained.test: no visible global function definition for ‘qchisq’
selfcontained.test: no visible global function definition for ‘cor’
selfcontained.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
CommT.anova: no visible global function definition for ‘aov’
CommT.legendpos: no visible global function definition for ‘quantile’
CommT.plotcolors: no visible global function definition for ‘hcl’
Undefined global functions or variables:
  aov hcl quantile
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("stats", "aov", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
Package suggested but not available for checking: ‘CAM’
compareC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
‘library’ or ‘require’ call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for ‘xmlRoot’
compareODM: no visible global function definition for ‘xmlTreeParse’
compareODM: no visible global function definition for ‘xmlChildren’
compareODM: no visible global function definition for ‘xmlAttrs’
compareODM: no visible global function definition for ‘xmlValue’
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Package in Depends field not imported from: ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for ‘grad’
dcomplnorm : f1: no visible global function definition for ‘dlnorm’
dcomplnorm : F1: no visible global function definition for ‘plnorm’
dcomplnorm : f1L: no visible global function definition for ‘dlnorm’
dcomplnorm : F1L: no visible global function definition for ‘plnorm’
pcomplnorm: no visible global function definition for ‘grad’
pcomplnorm : f1: no visible global function definition for ‘dlnorm’
pcomplnorm : F1: no visible global function definition for ‘plnorm’
pcomplnorm : F1L: no visible global function definition for ‘plnorm’
qcomplnorm: no visible global function definition for ‘grad’
qcomplnorm : f1: no visible global function definition for ‘dlnorm’
qcomplnorm : F1q: no visible global function definition for ‘qlnorm’
qcomplnorm : F1: no visible global function definition for ‘plnorm’
rcomplnorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
‘library’ or ‘require’ call to ‘hypergeo’ which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for ‘integrate’
pgfIhypergeometric: no visible global function definition for ‘uniroot’
pgfIhyperpoisson: no visible global function definition for ‘uniroot’
pgfIkattitypeh1: no visible global function definition for ‘uniroot’
pgfIkattitypeh2: no visible global function definition for ‘uniroot’
pgfIneymantypeb: no visible global function definition for ‘uniroot’
pgfIneymantypec: no visible global function definition for ‘uniroot’
pgfIpoissonlindley: no visible global function definition for ‘uniroot’
pgfIthomas: no visible global function definition for ‘uniroot’
pgfIwaring: no visible global function definition for ‘uniroot’
pgfIyule: no visible global function definition for ‘uniroot’
rCompound: no visible global function definition for ‘runif’
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/conclust.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
K1.norm: no visible global function definition for ‘dnorm’
K1.norm: no visible global function definition for ‘pnorm’
K1.t3: no visible global function definition for ‘pt’
K2.norm: no visible global function definition for ‘dnorm’
K2.norm: no visible global function definition for ‘pnorm’
K2.t3: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for ‘approx’
select_kmax: no visible global function definition for ‘median’
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
‘library’ or ‘require’ call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
‘library’ or ‘require’ calls in package code:
  ‘Rmpi’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for ‘makeCluster’
ConjointChecks: no visible global function definition for
  ‘clusterSetRNGStream’
ConjointChecks: no visible global function definition for
  ‘clusterApply’
ConjointChecks: no visible global function definition for ‘stopCluster’
omni.check: no visible global function definition for ‘runif’
omni.check: no visible global function definition for ‘quantile’
plot.checks: no visible global function definition for ‘mtext’
plot.checks: no visible global function definition for ‘text’
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Package version: 3.2.1
Unicode version: 13.0
ICU version: 67.1
Parallel computing: 4 of 32 threads used.
See https://quanteda.io for tutorials and examples.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Creating a dfm from a tokens input...
 ...lowercasing
 ...found 400 documents, 4,836 features
 ...complete, elapsed time: 0.199 seconds.
Finished constructing a 400 x 4,836 sparse dfm.
Could not fetch https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;1
HttpExceptionRequest Request {
  host                 = "latex.codecogs.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/png.image"
  queryString          = "?%5Cdpi%7B110%7D&space;%5Cbg_white&space;1"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "latex.codecogs.com" [Network.Socket.connect: <socket: 14>: does not exist (Connection refused)]))
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "points", "polygon",
             "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
advanceRNG: no visible global function definition for ‘runif’
randomEventMoves: no visible global function definition for ‘runif’
randomRescaledEventMoves: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  ‘write.table’
pvalue_calculator: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
compute.llh: no visible global function definition for ‘dnorm’
compute.u.hat.simple: no visible global function definition for ‘dnorm’
fit.CLM.1u.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start.NA: no visible global function definition for
  ‘kmeans’
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for ‘cor’
corr.Qmatrix: no visible global function definition for ‘cor.test’
summarise.Fst: no visible global function definition for ‘cor’
summarise.Fst: no visible global function definition for ‘sd’
summarise.lnPD: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Rd file 'corr.Qmatrix.Rd':
  \usage lines wider than 90 characters:
     corr.Qmatrix(filepath = "./", instruct = FALSE, rowncol = TRUE, avmax = TRUE, pvalue = FALSE, raw = TRUE, r = 0.99, p = 0.05)

Rd file 'rowncolMatrix-method.Rd':
  \examples lines wider than 100 characters:
     test <- rowncolMatrix(K = 3, filtermatrix = table(matrix(c("Y","Y","Y",NA,"Y","Y",NA,NA,"Y"),ncol = 3, byrow = TRUE)))

These lines will be truncated in the PDF manual.
dist: no visible global function definition for ‘quantile’
edgecount: no visible global function definition for ‘reshape’
edgecutoff: no visible global function definition for ‘boxplot’
edgecutoff: no visible global function definition for ‘sd’
edgecutoff: no visible global function definition for ‘median’
edgecutoff: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GA_search : subset_score: no visible global function definition for
  ‘combn’
choose_lambda : subset_score: no visible global function definition for
  ‘combn’
cond.fyx: no visible global function definition for ‘var’
cond.fyx: no visible global function definition for ‘cor’
diff_gen_PPI: no visible global function definition for ‘cov’
diff_gen_PPI: no visible global function definition for ‘sd’
f.test: no visible binding for global variable ‘var’
get_quantiles : node_edge: no visible global function definition for
  ‘combn’
score_scaling: no visible global function definition for ‘hist’
score_scaling: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
cosinor.lm: no visible binding for global variable ‘na.omit’
cosinor.lm: no visible global function definition for ‘terms’
cosinor.lm: no visible global function definition for ‘as.formula’
cosinor.lm: no visible global function definition for ‘lm’
cosinor_analyzer: no visible binding for global variable ‘vitamind’
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
D.M: no visible global function definition for ‘integrate’
lookbackTime: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Rd file 'mass.CO.Rd':
  \usage lines wider than 90 characters:
     mass.CO(intInt, z, alpha = 0.8, f.rest = 115.27, omega.m = 0.27, omega.lambda = 0.73, H.0 = 71)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rglpk’ ‘glmnet’ ‘parallel’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘countyflood.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for ‘model.response’
covLCA: no visible global function definition for ‘model.frame’
covLCA: no visible global function definition for ‘model.matrix’
covLCA: no visible global function definition for ‘rnorm’
covLCA: no visible global function definition for ‘flush.console’
covLCA: no visible global function definition for ‘ginv’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘as.formula’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit.data’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit’
covLCA.initialBeta: no visible global function definition for
  ‘as.formula’
covLCA.initialBeta: no visible global function definition for ‘poLCA’
covLCA.initialBeta: no visible global function definition for
  ‘mlogit.data’
covLCA.initialBeta: no visible global function definition for ‘mlogit’
covLCA.paramVariance: no visible global function definition for ‘ginv’
covLCA.varianceFirst: no visible global function definition for ‘bdiag’
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
covreg.mcmc: no visible global function definition for ‘model.frame’
covreg.mcmc: no visible global function definition for ‘model.matrix’
covreg.mcmc: no visible global function definition for ‘model.response’
covreg.mcmc: no visible global function definition for ‘lm’
covreg.mcmc: no visible global function definition for ‘rnorm’
covreg.mcmc: no visible global function definition for ‘cov’
rmn: no visible global function definition for ‘rnorm’
rwish: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
coxaalen: no visible global function definition for ‘terms’
coxaalen: no visible global function definition for ‘model.matrix’
coxaalen: no visible binding for global variable ‘frame’
coxaalen: no visible global function definition for ‘update.formula’
coxaalen: no visible global function definition for ‘capture.output’
coxdual: no visible global function definition for ‘terms’
coxdual: no visible global function definition for ‘model.matrix’
coxdual: no visible binding for global variable ‘frame’
coxdual: no visible global function definition for ‘update.formula’
coxdual: no visible global function definition for ‘as.formula’
coxdual: no visible global function definition for ‘capture.output’
frame.assign: no visible global function definition for ‘model.matrix’
linapprox: no visible global function definition for ‘approx’
print.coxinterval: no visible global function definition for ‘pchisq’
print.summary.coxinterval : f: no visible global function definition
  for ‘printCoefmat’
step2stepfun : f: no visible global function definition for ‘stepfun’
summary.coxinterval : f: no visible global function definition for
  ‘pchisq’
summary.coxinterval : f: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  approx as.formula capture.output frame model.matrix pchisq
  printCoefmat qnorm stepfun terms update.formula
Consider adding
  importFrom("graphics", "frame")
  importFrom("stats", "approx", "as.formula", "model.matrix", "pchisq",
             "printCoefmat", "qnorm", "stepfun", "terms",
             "update.formula")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for ‘model.extract’
coxr: no visible global function definition for ‘model.matrix’
coxr.draw: no visible global function definition for ‘lines’
coxr.draw: no visible global function definition for ‘points’
coxr.fit: no visible global function definition for ‘quantile’
gen_data: no visible global function definition for ‘rnorm’
gen_data: no visible global function definition for ‘rexp’
plot.coxr: no visible global function definition for ‘quantile’
plot.coxr: no visible global function definition for ‘par’
plot.coxr: no visible global function definition for ‘mtext’
plot.coxr: no visible global function definition for ‘title’
plot.coxr: no visible global function definition for ‘split.screen’
plot.coxr: no visible global function definition for ‘screen’
plot.coxr: no visible global function definition for ‘close.screen’
print.coxr: no visible global function definition for ‘pnorm’
print.coxr: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq pnorm
  points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
distance.comoving: no visible global function definition for
  ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘guidelines.Rmd’
‘library’ or ‘require’ call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘chron’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for ‘read.table’
collateDaily: no visible global function definition for ‘write.table’
collateHourly: no visible global function definition for ‘read.table’
collateHourly: no visible global function definition for ‘write.table’
downloadCRN: no visible global function definition for ‘download.file’
getUrlsCRN: no visible global function definition for ‘getURL’
writeDataset: no visible global function definition for ‘read.table’
writeDataset: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'downloadCRN.Rd':
  \usage lines wider than 90 characters:
     downloadCRN(url = CRN.DAILY.URL, directory = DAILY_DIR, years = seq(from = 2000, to = 2011, by = 1))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
'LazyData' is specified without a 'data' directory
get.plan: no visible global function definition for ‘menu’
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
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.
crossmatchtest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Rd file 'crossmatch-package.Rd':
  \examples lines wider than 100 characters:
                  c(0.03,0.11,0.16,-0.1,-0.05,0.16,0.12,0.4,0.04,0.71,0.01,0.21,-0.18,-0.08             ,-0.35,0.26,-0.6,-1.0))

Rd file 'crossmatchtest.Rd':
  \examples lines wider than 100 characters:
                  c(0.03,0.11,0.16,-0.1,-0.05,0.16,0.12,0.4,0.04,0.71,0.01,0.21,-0.18,-0.08             ,-0.35,0.26,-0.6,-1.0))

These lines will be truncated in the PDF manual.
BootC : BSs: no visible global function definition for ‘lm’
BootC : BSs: no visible global function definition for ‘vcov’
BootC: no visible global function definition for ‘boot’
BootC: no visible global function definition for ‘boot.ci’
DeltaC: no visible global function definition for ‘lm’
DeltaC: no visible global function definition for ‘vcov’
FiellerC: no visible global function definition for ‘lm’
FiellerC: no visible global function definition for ‘vcov’
nonLinearC: no visible global function definition for ‘nls’
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignettecrossrun.Rmd’
'LazyData' is specified without a 'data' directory
crrp: no visible global function definition for ‘approx’
gcrrp: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx
Consider adding
  importFrom("stats", "approx")
to your NAMESPACE file.
crrc: no visible binding for global variable ‘na.omit’
crrs: no visible binding for global variable ‘na.omit’
mycrr: no visible binding for global variable ‘na.omit’
mycrr.test: no visible binding for global variable ‘na.omit’
print.crrs: no visible global function definition for ‘pnorm’
psh.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
crrstep : crr.makecov1: no visible global function definition for
  ‘model.matrix’
crrstep : crr.dropterm: no visible global function definition for
  ‘terms’
crrstep : crr.dropterm: no visible global function definition for
  ‘as.formula’
crrstep : crr.addterm: no visible global function definition for
  ‘terms’
crrstep : crr.addterm: no visible global function definition for
  ‘as.formula’
crrstep: no visible global function definition for ‘as.formula’
crrstep: no visible global function definition for ‘terms’
crrstep: no visible global function definition for ‘model.frame’
crrstep: no visible binding for global variable ‘na.pass’
crrstep: no visible global function definition for ‘update’
crrstep: no visible global function definition for ‘drop.terms’
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
pielou: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
cstar: no visible global function definition for ‘vcov’
cstar : utility: no visible global function definition for ‘dt’
cstar : maximand: no visible global function definition for ‘integrate’
cstar: no visible global function definition for ‘uniroot’
cstari : utility: no visible global function definition for ‘dt’
cstari : maximand: no visible global function definition for
  ‘integrate’
cstari: no visible global function definition for ‘uniroot’
cstarme : utility: no visible global function definition for ‘density’
cstarme : maximand: no visible global function definition for
  ‘integrate’
cstarme : maximand: no visible global function definition for ‘sd’
cstarme: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘customsteps.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Cut: no visible global function definition for ‘cor’
MissSimulation: no visible global function definition for ‘rbinom’
cutoff: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
delta.glm: no visible global function definition for ‘glm’
delta.glm: no visible global function definition for ‘residuals’
delta.glm: no visible global function definition for ‘fitted’
delta.glm: no visible global function definition for ‘predict.glm’
two.stage.model.outputs: no visible global function definition for ‘sd’
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
calfun: no visible global function definition for ‘optim’
calfun: no visible global function definition for ‘cov’
calfun: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
func.constructRegressionFormula: no visible global function definition
  for ‘as.formula’
func.crossValidationAnalysis: no visible global function definition for
  ‘glm’
func.crossValidationAnalysis: no visible global function definition for
  ‘predict’
func.crossValidationAnalysis: no visible global function definition for
  ‘write.table’
func.externalValidationAnalysis: no visible global function definition
  for ‘predict’
func.externalValidationAnalysis: no visible global function definition
  for ‘write.table’
func.linearRegressionAnalysis: no visible global function definition
  for ‘glm’
func.linearRegressionAnalysis: no visible global function definition
  for ‘predict’
func.linearRegressionAnalysis: no visible global function definition
  for ‘write.table’
func.sortDataColumns: no visible global function definition for
  ‘write.table’
mainfunc.q2: no visible global function definition for ‘write.table’
mainfunc.q2: no visible global function definition for ‘new’
mainfunc.stats: no visible global function definition for ‘write.table’
mainfunc.stats: no visible global function definition for ‘new’
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cvimpute.by.wavelet: no visible global function definition for ‘sd’
cvimpute.by.wavelet: no visible global function definition for ‘mad’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘sd’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘mad’
cvwavelet.image.after.impute: no visible global function definition for
  ‘sd’
cvwavelet.image.after.impute: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
random.CV: no visible global function definition for ‘var’
regular.CV: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'gurobi', 'rcbc'
Found the following files/directories:
  ‘tex.table.tex’
.mixgauss_init: no visible global function definition for ‘cov’
.mixgauss_init: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
cxxfun.from.dll: no visible global function definition for ‘new’
cxxfun.from.dso.bin: no visible global function definition for ‘new’
cxxfunctionplus: no visible global function definition for ‘getPlugin’
cxxfunctionplus: no visible global function definition for
  ‘cxxfunction’
cxxfunctionplus: no visible global function definition for ‘new’
show,cxxdso: no visible global function definition for ‘object.size’
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘fda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for ‘na.omit’
get.breaks.vector: no visible global function definition for ‘na.omit’
get.cycle.breaks: no visible global function definition for ‘na.omit’
get.cycle.counts: no visible global function definition for ‘na.omit’
get.cycle.matrix: no visible global function definition for ‘na.omit’
get.cycle.minimums: no visible global function definition for ‘na.omit’
get.peaks: no visible global function definition for ‘embed’
get.trans: no visible global function definition for
  ‘create.bspline.basis’
get.trans: no visible global function definition for ‘smooth.basis’
get.trans: no visible global function definition for ‘deriv.fd’
get.trans: no visible global function definition for ‘eval.fd’
get.transition.locations: no visible global function definition for
  ‘na.omit’
get.transition.locations.FDiff: no visible global function definition
  for ‘na.omit’
get.window: no visible global function definition for ‘sd’
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
cytoDiv: no visible global function definition for ‘colorRampPalette’
cytoDiv: no visible global function definition for ‘persp’
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
Rd file 'cytoDiv.Rd':
  \usage lines wider than 90 characters:
     cytoDiv(df, x.var="fsc_small", y.var="chl_small", Ncat = 16, Nbit = 16, do.plot=FALSE, ...)
  \examples lines wider than 100 characters:
     rainbow.cols <- colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow","#FF7F00", "red", "#7F0000"))
     plot(cleaned.df[,2], cleaned.df[,3], col= densCols(cleaned.df[,2], cleaned.df[,3], colramp = rainbow.cols))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘GRCh38_browser’ ‘GRCh38_map’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'intPlot.Rd':
  \usage lines wider than 90 characters:
      intPlot(y, fac1 = NULL, fac2 = NULL, xlab = NULL, xlab2 = NULL, ylab = NULL, data.order=TRUE, exlim=0.1, jitter=0.02, conf.level=0.95, ... [TRUNCATED]
      intPlot(y, data, xlab = NULL, xlab2 = NULL, ylab = NULL, data.order = TRUE, exlim=0.1, jitter=0.02, conf.level=0.95, interval.type="tu ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
dashboard_open: no visible global function definition for ‘write.csv’
dashboard_open: no visible global function definition for
  ‘capture.output’
dctable: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘datadigest.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
dbEmpLikeGOF: no visible global function definition for ‘runif’
dbEmpLikeGOF: no visible global function definition for ‘var’
dbEmpLikeGOF: no visible global function definition for ‘rnorm’
emplikeGOFinternal: no visible global function definition for ‘var’
getCutoff: no visible binding for global variable ‘unifCut’
getCutoff: no visible binding for global variable ‘normCut’
getCutoff: no visible global function definition for ‘lm’
getCutoff: no visible binding for global variable ‘distEqCut’
getPval: no visible binding for global variable ‘unifCut’
getPval: no visible binding for global variable ‘normCut’
getPval: no visible global function definition for ‘lm’
getPval: no visible binding for global variable ‘distEqCut’
helperPval: no visible global function definition for ‘lm’
returnCutoff: no visible global function definition for ‘quantile’
testfun2: no visible global function definition for ‘runif’
testfun2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
computePval: no visible global function definition for ‘lm’
computeQhat: no visible global function definition for ‘pnorm’
dbELnorm: no visible global function definition for ‘rnorm’
getCutoffTableThree: no visible global function definition for ‘lm’
getCutoffTableTwo: no visible global function definition for ‘lm’
getCutoffValue: no visible global function definition for ‘lm’
helperGetTstat: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘quantile’
varianceEstimator: no visible global function definition for ‘density’
varianceEstimator: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
‘library’ or ‘require’ call to ‘fdrtool’ which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for ‘sd’
avelinkdis: no visible global function definition for ‘dist’
centdis: no visible global function definition for ‘sd’
centdis: no visible global function definition for ‘dist’
distable: no visible global function definition for ‘write.table’
functionall: no visible global function definition for ‘read.table’
randdis: no visible global function definition for ‘write.table’
valuep: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
Rd file 'distable.Rd':
  \examples lines wider than 100 characters:
     ##before using "b1.txt" data, we need to find "b1.txt" in the data file and  put it in the work space of R

Rd file 'functionall.Rd':
  \examples lines wider than 100 characters:
     ##before running this funtion, we need to find out "b1.txt" data file, and put it into the R workspace.
     functionall(system.file("data","b1.txt",package="DBGSA"),10,avelinkdis,"euclidean","distance",afExp,2000,10,"rand.txt","pvalue.txt")

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘LFC.d.jpeg’ ‘LFC.s.jpeg’ ‘TF_bridged_DCL.pdf’
  ‘TF_bridged_DCL_int.pdf’
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’
  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: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines runif
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis pnorm qchisq sd vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘decomposedPSF-vignette.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
‘library’ or ‘require’ call to ‘klaR’ which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for ‘J’
.makeICCDialog: no visible global function definition for ‘new’
.makeICCDialog: no visible global function definition for ‘.jnull’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘new’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘J’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘new’
.makeNewLDADialog: no visible global function definition for ‘J’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘new’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘toJava’
.makeNewReliabilityDialog: no visible global function definition for
  ‘new’
.makeNewReliabilityDialog: no visible global function definition for
  ‘toJava’
.onLoad: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘jgr.getMenuNames’
.onLoad: no visible global function definition for ‘jgr.insertMenu’
.onLoad: no visible global function definition for ‘jgr.addMenu’
.onLoad: no visible global function definition for ‘jgr.addMenuItem’
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
.makeQuickWordcloud: no visible global function definition for ‘J’
.makeQuickWordcloud: no visible global function definition for ‘new’
.makeQuickWordcloud: no visible global function definition for ‘.jnull’
.makeTextPlot: no visible global function definition for ‘J’
.makeTextPlot: no visible global function definition for ‘new’
.makeTextPlot: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘.jpackage’
.onLoad: no visible global function definition for ‘.jnew’
.onLoad: no visible global function definition for ‘J’
make.color.scale: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
binary.state: no visible global function definition for ‘runif’
dbn.dnn.train: no visible global function definition for ‘runif’
dropout.mask: no visible global function definition for ‘runif’
nn.train: no visible global function definition for ‘runif’
rbm.train: no visible global function definition for ‘runif’
sae.dnn.train: no visible global function definition for ‘runif’
show.digit: no visible global function definition for ‘gray’
show.digit: no visible global function definition for ‘image’
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
DEEPR : perm_function: no visible global function definition for ‘head’
DEEPR : perm_function: no visible global function definition for ‘tail’
simCophy: no visible global function definition for ‘rpois’
simCophy: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
DendSer: no visible global function definition for ‘getFromNamespace’
crit2cost : <anonymous>: no visible global function definition for
  ‘as.dist’
dser.dist: no visible global function definition for ‘hclust’
dser.matrix: no visible global function definition for ‘dist’
plotAsColor: no visible global function definition for ‘image’
plotAsColor: no visible global function definition for ‘box’
plotAsColor: no visible global function definition for ‘axis’
seriation_method_dist_dser: no visible global function definition for
  ‘hclust’
seriation_method_dist_dser: no visible global function definition for
  ‘modifyList’
seriation_method_leafsort: no visible global function definition for
  ‘modifyList’
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
ds: no visible global function definition for ‘is.ts’
ds: no visible global function definition for ‘frequency’
getds: no visible global function definition for ‘resid’
getds: no visible global function definition for ‘lm.fit’
getds: no visible global function definition for ‘sd’
getds: no visible global function definition for ‘var’
getds: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
Rd file 'ds.Rd':
  \usage lines wider than 90 characters:
     ds(z, Fm = 6, Fs = 6, type = c("daily", "monthly"), searchQ=TRUE, lag.max=20, ic=c("BIC","AIC"), standardizeQ=TRUE)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘myDesignGGSAplot.png’ ‘myDesignGG_arrayDesign.csv’
  ‘myDesignGG_conditionDesign.csv’
Package which this enhances but not available for checking: ‘gurobi’
Malformed Description field: should contain one or more complete sentences.
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Rd file 'EPS.value.Rd':
  \examples lines wider than 100 characters:
     co021.subset<-co021.subset[,-c(28,30,31)] ## to remove the following series "645232","646107" and "646118"

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘data’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rbinom’
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rnorm’
simulate_dataframe : generate_initial: no visible global function
  definition for ‘rbinom’
simulate_dataframe: no visible binding for global variable ‘randu’
simulate_dataframe: no visible global function definition for ‘rbinom’
simulate_dataframe: no visible global function definition for ‘rnorm’
simulate_dataframe: no visible global function definition for ‘rpois’
simulate_dataframe : add_NAs: no visible global function definition for
  ‘rbinom’
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘integrate’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘dchisq’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘nlm’
cvm.test : cvm.stat.disc: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘runif’
cvm.test: no visible global function definition for ‘is.stepfun’
cvm.test: no visible global function definition for ‘knots’
ks.test : exact.pval : ts.pval: no visible global function definition
  for ‘ecdf’
ks.test : sim.pval: no visible global function definition for ‘runif’
ks.test : sim.pval : getks: no visible global function definition for
  ‘ecdf’
ks.test: no visible global function definition for ‘is.stepfun’
ks.test: no visible global function definition for ‘knots’
ks.test: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
dichromat: no visible global function definition for ‘col2rgb’
dichromat: no visible global function definition for ‘predict’
dichromat: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for ‘txtProgressBar’
le.pesquisa: no visible global function definition for ‘type.convert’
le.pesquisa: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
L2eV: no visible binding for global variable ‘constants’
L2w: no visible binding for global variable ‘constants’
dielectric: no visible global function definition for ‘new’
dielectric2plot: no visible global function definition for ‘reshape’
eV2L: no visible binding for global variable ‘constants’
t2eV: no visible binding for global variable ‘constants’
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘module_list.txt’ ‘res.txt’
Packages in Depends field not imported from:
  ‘PropCIs’ ‘gee’ ‘rootSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for ‘diffpropci.Wald.mp’
diffpci: no visible global function definition for ‘diffpropci.mp’
diffpci: no visible global function definition for ‘scoreci.mp’
exact.cond : exactci: no visible global function definition for ‘qf’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : one.ci: no visible global function definition
  for ‘uniroot’
np.nv: no visible global function definition for ‘qnorm’
np.t: no visible global function definition for ‘qt’
uncond: no visible global function definition for ‘qnorm’
wald.cc: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘uniroot.all’
wilson.cc: no visible global function definition for ‘qnorm’
wilson.cc: no visible global function definition for ‘uniroot.all’
wilson.phi: no visible global function definition for ‘qnorm’
wilson.phi: no visible global function definition for ‘uniroot.all’
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
p.discrete.adjust : <anonymous>: no visible global function definition
  for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
value: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'dualFlashlight.fn.Rd':
  \usage lines wider than 90 characters:
     dualFlashlight.fn(result.df, wellName = "WELL_USAGE", x.name = "mean", y.name = "ssmd", sampleName = "Sample", sampleColor = "black", c ... [TRUNCATED]

Rd file 'imageDesign.fn.Rd':
  \usage lines wider than 90 characters:
     imageDesign.fn(dataOnePlate.df, wellName = NA, rowName, colName, wells = NULL, colors = NULL, title = " ")

Rd file 'imageIntensity.fn.Rd':
  \usage lines wider than 90 characters:
     imageIntensity.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, sampleName = "Sample", ... [TRUNCATED]

Rd file 'plateWellSeries.fn.Rd':
  \usage lines wider than 90 characters:
     plateWellSeries.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, show.wellTypes = NULL ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
densest: no visible global function definition for ‘weighted.mean’
diss: no visible global function definition for ‘cov’
neighbors: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘csim’ ‘xyz’ ‘xyz.sav’ ‘xyz.sav.comment’
Found the following files/directories:
  ‘csim.mean’ ‘csim.mean.comment’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BOLTSSIRR’
Packages suggested but not available for checking: 'sendplot', 'HWxtest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
DNMF: no visible global function definition for ‘runif’
NMFpval: no visible global function definition for ‘p.adjust’
ndNMF: no visible global function definition for ‘runif’
rnk: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ppert: no visible global function definition for ‘pbeta’
prepare8pkg: no visible global function definition for ‘glob2rx’
qpert: no visible global function definition for ‘qbeta’
rpert: no visible global function definition for ‘rbeta’
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘documenter.Rmd’
Found the following files/directories:
  ‘annotation_file.yml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Suggests orphaned package: ‘bibtex’
Package suggested but not available for checking: ‘DiPs’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
dostats: no visible binding for global variable ‘na.fail’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
pval.default: no visible global function definition for ‘.hasSlot’
pval.lm: no visible global function definition for ‘anova’
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘OpenMPController’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘dotdot.Rmd’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
compute_xsq: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
DSBayes: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘coef’
DSBayes: no visible global function definition for ‘vcov’
DSBayes : MLE: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘integrate’
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for ‘dnorm’
DSBayes : ds.numer: no visible global function definition for
  ‘integrate’
DSBayes : lower: no visible global function definition for ‘qlogis’
DSBayes : lower: no visible global function definition for ‘integrate’
DSBayes : upper: no visible global function definition for ‘qlogis’
DSBayes : upper: no visible global function definition for ‘integrate’
DSBayes: no visible global function definition for ‘optimize’
DSBayes: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
DCEA: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘pdf’
DS: no visible global function definition for ‘dev.off’
LFC: no visible global function definition for ‘glm’
LFC: no visible global function definition for ‘predict’
PartialCor: no visible global function definition for ‘na.omit’
comDCGLplot: no visible global function definition for ‘pdf’
comDCGLplot: no visible global function definition for ‘dev.off’
percentLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘pt’
qLinkfilter: no visible global function definition for ‘p.adjust’
rLinkfilter: no visible global function definition for ‘cor’
varianceBasedfilter: no visible binding for global variable ‘var’
varianceBasedfilter: no visible global function definition for ‘median’
varianceBasedfilter: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf predict pt var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
DLR: no visible global function definition for ‘formula’
DLR: no visible global function definition for ‘terms’
DLR: no visible global function definition for ‘model.matrix’
DLR: no visible global function definition for ‘as.formula’
DLR: no visible binding for global variable ‘binomial’
DLR: no visible global function definition for ‘coef’
DLR: no visible global function definition for ‘pnorm’
DLR: no visible global function definition for ‘qnorm’
acc.1test: no visible global function definition for ‘qnorm’
pv.gs: no visible global function definition for ‘pchisq’
pv.rpv: no visible global function definition for ‘qnorm’
pv.rpv: no visible global function definition for ‘pnorm’
pv.wgs: no visible global function definition for ‘pchisq’
sesp.diff.ci: no visible global function definition for ‘qnorm’
sesp.mcnemar: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  as.formula binomial coef formula model.matrix pchisq pnorm qnorm
  terms
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "formula",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignette.Rmd’
'LazyData' is specified without a 'data' directory
DTK.plot: no visible global function definition for ‘axis’
DTK.plot: no visible global function definition for ‘title’
DTK.plot: no visible global function definition for ‘lines’
DTK.plot: no visible global function definition for ‘points’
DTK.test: no visible binding for global variable ‘sd’
DTK.test: no visible global function definition for ‘qtukey’
TK.test: no visible global function definition for ‘TukeyHSD’
TK.test: no visible global function definition for ‘aov’
Undefined global functions or variables:
  TukeyHSD aov axis lines points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File
  LICENSE
is not mentioned in the DESCRIPTION file.
dummy: no visible global function definition for ‘model.matrix’
dummy: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
Rd file 'dummy.Rd':
  \usage lines wider than 90 characters:
     dummy.data.frame(data, names = NULL, omit.constants=TRUE, dummy.classes = getOption("dummy.classes"), all = TRUE, ...)

These lines will be truncated in the PDF manual.
cvSDDT: no visible global function definition for ‘qt’
cvSDDT : Cj_SD.fun: no visible global function definition for ‘combn’
cvSDDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘rnorm’
cvSUDT: no visible global function definition for ‘rchisq’
cvSUDT : psi.fun: no visible global function definition for ‘pnorm’
cvSUDT: no visible global function definition for ‘qt’
cvSUDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘combn’
nvDT : samplesize: no visible global function definition for ‘rnorm’
nvDT : samplesize: no visible global function definition for ‘rchisq’
nvDT : samplesize: no visible global function definition for ‘pnorm’
nvDT : ssBonf: no visible global function definition for ‘qnorm’
nvDT : ssBonf: no visible global function definition for ‘qt’
nvDT : ssBonf: no visible global function definition for ‘rnorm’
nvDT : ssBonf: no visible global function definition for ‘rchisq’
nvDT : ssBonf: no visible global function definition for ‘pnorm’
nvDT: no visible global function definition for ‘uniroot’
powDT: no visible global function definition for ‘rnorm’
powDT: no visible global function definition for ‘rchisq’
powDT: no visible global function definition for ‘pnorm’
qvSDDT: no visible global function definition for ‘pt’
qvSUDT: no visible global function definition for ‘rnorm’
qvSUDT: no visible global function definition for ‘rchisq’
qvSUDT : psi.fun: no visible global function definition for ‘pnorm’
qvSUDT: no visible global function definition for ‘pt’
qvSUDT : Pj.fun: no visible global function definition for ‘qt’
qvSUDT : Pj.fun: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn pnorm pt qnorm qt rchisq rnorm uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "qnorm", "qt", "rchisq", "rnorm",
             "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Clough: no visible global function definition for ‘dgamma’
computePosterior,Counts: no visible global function definition for
  ‘dnbinom’
getPosteriorParam,Counts: no visible global function definition for
  ‘qgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘dgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘pgamma’
plotPosterior,Counts: no visible global function definition for ‘axis’
plotPosterior,Counts: no visible global function definition for
  ‘abline’
plotPosterior,Counts: no visible global function definition for ‘lines’
plotPosterior,Counts: no visible global function definition for ‘rect’
plotPosterior,Counts: no visible global function definition for ‘curve’
plotPosterior,Counts: no visible global function definition for
  ‘dgamma’
plotPosterior,Counts: no visible global function definition for
  ‘legend’
show,Counts: no visible global function definition for ‘head’
show,Counts: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline axis curve dgamma dnbinom head legend lines pgamma qgamma rect
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "rect")
  importFrom("stats", "dgamma", "dnbinom", "pgamma", "qgamma")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for ‘pchisq’
RunClustering : CheckClusterNew: no visible global function definition
  for ‘qchisq’
RunClustering: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘var’
RunDenoising: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘median’
RunDenoising: no visible global function definition for ‘var’
RunDenoising : buildEstimate: no visible global function definition for
  ‘qchisq’
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GetIntMod: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘logLik’
GetPV: no visible global function definition for ‘optimize’
GetPV: no visible global function definition for ‘pchisq’
fitdi: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
eb: no visible global function definition for ‘optimize’
ebalance: no visible global function definition for ‘var’
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
'LazyData' is specified without a 'data' directory
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
dilution: no visible global function definition for ‘grey’
dilution: no visible global function definition for ‘lines’
dilution: no visible global function definition for ‘rect’
dilution: no visible global function definition for ‘segments’
dilution: no visible global function definition for ‘text’
dilution: no visible global function definition for ‘arrows’
pricefit: no visible global function definition for ‘runif’
Undefined global functions or variables:
  arrows grey lines rect runif segments text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "arrows", "lines", "rect", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
plot.ETdiagnosis: no visible global function definition for ‘par’
plot.ETdiagnosis: no visible global function definition for ‘lines’
plot.ETdiagnosis: no visible global function definition for ‘legend’
plot.ETmain: no visible global function definition for ‘par’
plot.ETmain: no visible global function definition for ‘polygon’
plot.ETmain: no visible global function definition for ‘axis’
plot.ETmain: no visible global function definition for ‘legend’
plot.ETmain: no visible global function definition for ‘lines’
plot.Transpose: no visible global function definition for ‘par’
plot.Transpose: no visible global function definition for ‘polygon’
plot.Transpose: no visible global function definition for ‘axis’
plot.Transpose: no visible global function definition for ‘legend’
plot.smooth: no visible global function definition for ‘lines’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘par’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘rainbow’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘filled.contour’
regPB: no visible global function definition for ‘coef’
regPB: no visible global function definition for ‘lm’
regPB.ac: no visible global function definition for ‘coef’
regPB.ac: no visible global function definition for ‘lm’
regPB.ctsa: no visible global function definition for ‘coef’
regPB.ctsa: no visible global function definition for ‘lm’
Undefined global functions or variables:
  axis coef filled.contour legend lines lm par polygon rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "filled.contour", "legend", "lines",
             "par", "polygon")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘spc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'ecoCusum.Rd':
  \examples lines wider than 100 characters:
     ## global optimization to h, H and n, when lambda = 0.01, "Nelder-Mead" optimization algorithm doesn't work

Rd file 'ecoEwma.Rd':
  \examples lines wider than 100 characters:
     #yy = ecoEwma(h = seq(.7,1,by=.01), w = seq(0.8,1,by=.01),k = seq(2.9,3.3, by = 0.01), n = 4:5, P0 = 110, P1 = 10, Cf = 50, contour.plo ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tmplp.dat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
UCexactTest: no visible global function definition for ‘is’
UCexactTest: no visible global function definition for ‘new’
pvalue: no visible global function definition for ‘dnbinom’
pvalue: no visible global function definition for ‘pnbinom’
sup.mu: no visible global function definition for ‘predict’
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
geteegdata: no visible global function definition for ‘untar’
geteegdata: no visible global function definition for ‘read.table’
geteegdata: no visible global function definition for ‘write.csv’
geteegdata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/eel.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
eiginv: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for ‘cov’
boot_pr_comp: no visible global function definition for ‘quantile’
boot_pr_comp: no visible global function definition for ‘segments’
boot_pr_comp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘class’ ‘quantreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for ‘kmeans’
cluster.segment: no visible global function definition for ‘knn’
comp.anc.dist: no visible global function definition for ‘wilcox.test’
eila: no visible global function definition for ‘hasArg’
get.prob.score: no visible global function definition for ‘glm’
get.prob.score: no visible global function definition for ‘binomial’
get.prob.score: no visible binding for global variable ‘logit’
get.prob.score: no visible global function definition for ‘predict’
quantreg.est: no visible global function definition for ‘rnorm’
quantreg.est: no visible global function definition for ‘rq.fit.fnb’
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'KM.audit.Rd':
  \usage lines wider than 90 characters:
     KM.audit(data, U, Z, alpha = 0.25, plot = FALSE, debug = FALSE, return.Ps = FALSE, truncate.Ps = TRUE)

Rd file 'make.audit.Rd':
  \usage lines wider than 90 characters:
     make.audit(Z = NULL, method = c("tweak", "opt.bad", "opt.bad.WPM", "opt.bad.packed", "opt.bad.packed.WPM", "ok", "no error"), p_d = 0.2 ... [TRUNCATED]

Rd file 'make.opt.packed.bad.Rd':
  \usage lines wider than 90 characters:
     make.opt.packed.bad(Z, max.taint = 1, max.taint.good = max.taint, WPM = FALSE, add.good = 0, add.random = FALSE)

Rd file 'simulateIt.Rd':
  \usage lines wider than 90 characters:
     simulateIt(data, M = 50, alpha = 0.25, plot = FALSE, debug = FALSE, return.Ps = FALSE, truncate.Ps = TRUE)

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: ‘elec’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BaB: no visible binding for global variable ‘calc.pairwise.e_p’
BaB: no visible global function definition for ‘weight.function’
BaB: no visible global function definition for ‘compute.stark.t’
LKPBound: no visible binding for global variable ‘calc.pairwise.e_p’
LKPBound: no visible global function definition for ‘weight.function’
LKPBound: no visible global function definition for ‘compute.stark.t’
eqValBound: no visible binding for global variable ‘calc.pairwise.e_p’
eqValBound: no visible global function definition for ‘weight.function’
eqValBound: no visible global function definition for ‘compute.stark.t’
getEbsMargin: no visible global function definition for ‘is.elec.data’
getEbsMargin: no visible global function definition for
  ‘maximumMarginBound’
makeStratObj: no visible global function definition for ‘is.elec.data’
makeStratObj: no visible global function definition for
  ‘maximumMarginBound’
strat.elec.data: no visible global function definition for ‘elec.data’
takeOutZeroMMB: no visible global function definition for
  ‘maximumMarginBound’
withReplaceBound: no visible binding for global variable
  ‘calc.pairwise.e_p’
withReplaceBound: no visible global function definition for
  ‘weight.function’
withReplaceBound: no visible global function definition for
  ‘compute.stark.t’
Undefined global functions or variables:
  calc.pairwise.e_p compute.stark.t elec.data is.elec.data
  maximumMarginBound weight.function
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Likelihood: no visible global function definition for
  ‘makePSOCKcluster’
Likelihood: no visible global function definition for ‘clusterExport’
Likelihood: no visible global function definition for ‘makeForkCluster’
Likelihood.first.run: no visible global function definition for
  ‘clusterApply’
Likelihood.next.runs: no visible global function definition for
  ‘clusterApply’
es.stopCluster: no visible global function definition for ‘stopCluster’
plot.es.pedigree: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘PPtree’
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘etc’
Packages in Depends field not imported from:
  ‘MASS’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘eixport’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
‘library’ or ‘require’ call to ‘reshape’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MFFetch: no visible global function definition for ‘melt’
Undefined global functions or variables:
  melt
Rd file 'emme2.Rd':
  \usage lines wider than 90 characters:
          write.mf(data, numname, bank, file0, mcent, mmat, mat.dir, newname=NULL, newdesc=NULL)
  \examples lines wider than 100 characters:
          x <- matrix(rnorm(mf2), nrow(mf2), ncol(mf2)) #Random generate length(mf) numbers to write dummy data to bank
          write.mf(x, 2, "emme2/emme2ban", file0, file1$global["mcent"], file1$global["mmat"], mat.dir, newname="test", newdesc="test matrix ... [TRUNCATED]
          link.data <- read.link.data("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])
          nodes <- read.nodes("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
empiricalFDR: no visible global function definition for ‘axis’
empiricalFDR: no visible global function definition for ‘loess’
empiricalFDR: no visible global function definition for ‘predict’
empiricalFDR: no visible global function definition for ‘lines’
empiricalFDR: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘axis’
fdrBiCurve: no visible global function definition for ‘lines’
fdrBiCurve: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘legend’
simulateCounts: no visible global function definition for
  ‘txtProgressBar’
simulateCounts: no visible global function definition for
  ‘setTxtProgressBar’
simulateCounts: no visible global function definition for ‘rnorm’
simulateCounts: no visible global function definition for ‘hist’
simulateCounts: no visible global function definition for ‘colData’
Undefined global functions or variables:
  abline axis colData hist legend lines loess predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Found the following files/directories:
  ‘somefile’
Package suggested but not available for checking: ‘SPECIES’
Unknown package ‘SPECIES’ in Rd xrefs
diffcv: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘fligner.test’
diffcvall: no visible global function definition for ‘p.adjust’
diffcvpFK: no visible global function definition for ‘fligner.test’
diffcvpFK: no visible global function definition for ‘p.adjust’
diffexp: no visible global function definition for ‘var’
diffexp: no visible global function definition for ‘t.test’
diffexp: no visible global function definition for ‘p.adjust’
diffexp2: no visible global function definition for ‘var’
diffexp2: no visible global function definition for ‘t.test’
diffexp2: no visible global function definition for ‘p.adjust’
diffnsepperm: no visible global function definition for ‘p.adjust’
diffseall: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘plotrix’ which was already attached by Depends.
  Please remove these calls from your code.
‘library’ or ‘require’ calls in package code:
  ‘Hmisc’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘a.alpha.ade’ ‘a.coladd.ade’ ‘a.getcol.ade’ ‘a.glc’
Rd file 'scatter.ade.Rd':
  \examples lines wider than 100 characters:
     scatter.ade(x, y, g, z, vnames=c("blue","red"), alpha=0.25, xlim=c(-5, 5), zticks=c(1, 2, 3, 4, 5), wall=3)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘EpiSoon’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
plot.episplineDensity: no visible global function definition for
  ‘points’
postproc: no visible global function definition for ‘points’
preprocess.data: no visible global function definition for ‘sd’
Undefined global functions or variables:
  points sd
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
eqs2lavaan: no visible global function definition for ‘ignore.case’
eqs2lavaan: no visible global function definition for ‘str_join’
eqs2lavaan: no visible binding for global variable ‘r’
eqsCorr: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘par’
plotCov: no visible global function definition for ‘image’
plotCov: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Supplementary_Materials.Rmd’ using rmarkdown
Loading required package: lavaan
This is lavaan 0.6-10
lavaan is FREE software! Please report any bugs.
File ../../../doc/html/prism.js not found in resource path
Error: processing vignette ‘Supplementary_Materials.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘Supplementary_Materials.Rmd’

SUMMARY: processing the following file failed:
  ‘Supplementary_Materials.Rmd’

Error: Vignette re-building failed.
Execution halted
The following files contain a license that requires
distribution of original sources:
  ‘upgreek.sty’
Please ensure that you have complied with it.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexpected end of input (in ' quoted string opened at ergm-terms.Rd:2227:60)
problem found in ‘ergm-terms.Rd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘errorize.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis points title var
Consider adding
  importFrom("graphics", "axis", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ESEA.Main: no visible global function definition for ‘rnorm’
ESEA.Main: no visible global function definition for ‘sd’
ESEA.Main: no visible global function definition for ‘p.adjust’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘lines’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘colors’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘points’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘legend’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘text’
PlotPathwayGraph: no visible global function definition for ‘par’
PlotRunEnrichment: no visible global function definition for ‘lines’
PlotRunEnrichment: no visible global function definition for ‘colors’
PlotRunEnrichment: no visible global function definition for ‘text’
SavePathway2File: no visible global function definition for ‘is’
calEdgeCorScore: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estoutstorage’
descsto: 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').
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Undefined global functions or variables:
  hist rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/etma.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘eudract.Rmd’ using rmarkdown
File ../../../doc/html/prism.js not found in resource path
Error: processing vignette ‘eudract.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘eudract.Rmd’

SUMMARY: processing the following file failed:
  ‘eudract.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
percentdiff.evaluate.core.Rd:26-31: Must contain verbatim text
problem found in ‘percentdiff.evaluate.core.Rd’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
powerSet : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
mposterior: no visible global function definition for ‘optim’
rl.pred: no visible global function definition for ‘matplot’
rl.pst: no visible binding for global variable ‘quantile’
rl.pst: no visible global function definition for ‘matplot’
Undefined global functions or variables:
  matplot optim quantile
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘sample .nwk’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘UsingEvolutionaryGames.Rmd’
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘evd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DPOT: no visible global function definition for ‘optim’
mop.rho: no visible global function definition for ‘median’
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BinomialCIone: no visible global function definition for ‘na.omit’
PairedCIone: 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.
Malformed Description field: should contain one or more complete sentences.
build.mcx.obj: no visible global function definition for ‘glm’
build.mcx.obj: no visible binding for global variable ‘poisson’
build.mcx.obj: no visible global function definition for ‘fitted’
cab: no visible global function definition for ‘rbinom’
cab: no visible global function definition for ‘runif’
mcexact: no visible global function definition for ‘update’
rounded.tprob: no visible global function definition for ‘pt’
simtable.cab: no visible global function definition for ‘rbinom’
simtable.cab: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ExactData’
plot.pgrid: no visible global function definition for ‘image’
statistic.cv: no visible global function definition for ‘quantile’
statistic.sim: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘Vignette.Rmd’
Malformed Description field: should contain one or more complete sentences.
index.citations: no visible global function definition for
  ‘txtProgressBar’
read.exsic: no visible global function definition for ‘read.csv’
update.pb: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "polygon",
             "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
exbio: no visible global function definition for ‘as.formula’
exbio: no visible global function definition for ‘glm’
exbio: no visible binding for global variable ‘gaussian’
exbio: no visible global function definition for ‘Gamma’
exbio: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
Rd file 'exbio.Rd':
  \usage lines wider than 90 characters:
     exbio(R, R.alt, cc, n, tol = 0.001, a.start = 1, b.start = 1, max.it = 1000, digits = NULL, model.maf = TRUE)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
font_install: no visible global function definition for
  ‘installed.packages’
font_install: no visible global function definition for
  ‘install.packages’
fonttable_add: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
toJavaMatrix2D: 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').
Found the following files/directories:
  ‘temp.Rdata’
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: ‘exuberdata’
Malformed Description field: should contain one or more complete sentences.
Rd file 'distance2point.Rd':
  \usage lines wider than 90 characters:
     distance2point(x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
  \examples lines wider than 100 characters:
     function( x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight ) {

Rd file 'subtendedAngle.Rd':
  \usage lines wider than 90 characters:
     subtendedAngle(x1, y1, x2, y2, viewerDistance = 58.74, viewerHeight = 4.55, resolutionX = 1280, resolutionY = 1024, screenWidth = 33.97 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     function( x1, y1, x2, y2, viewerDistance=58.74, viewerHeight=4.55, resolutionX=1280, resolutionY=1024, screenWidth=33.97, screenHeight= ... [TRUNCATED]
         d1 <- distance2point(x1, y1, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
         d2 <- distance2point(x2, y2, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gibbs2: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_30iter.RData’ ‘test_50iter.RData’ ‘test_v2_50iter.RData’
Malformed Description field: should contain one or more complete sentences.
fma: no visible global function definition for ‘factanal’
fma: no visible global function definition for ‘runif’
fma: no visible global function definition for ‘kmeans’
fma: no visible global function definition for ‘var’
fma.em.alg: no visible global function definition for ‘var’
misc : q: no visible global function definition for ‘name’
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Rd file 'fma.Rd':
  \usage lines wider than 90 characters:
     fma(y, k, r, x.z = NULL, x.w = NULL, it = 15, eps = 1e-04, seed = 4, scaling = FALSE, init = NULL)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘FCMgraph.jpg’
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in ‘?.onAttach’.
'LazyData' is specified without a 'data' directory
coef.FAMILY: no visible global function definition for ‘glm’
coef.FAMILY: no visible global function definition for ‘lm’
fm2v: no visible global function definition for ‘na.omit’
l_inf_prox: no visible global function definition for ‘tail’
predict.FAMILY: no visible global function definition for ‘coef’
predict.FAMILY: no visible global function definition for ‘lm’
predict.FAMILY: no visible global function definition for ‘predict’
predict.FAMILY: no visible global function definition for ‘glm’
predict.FAMILY: no visible global function definition for ‘predict.glm’
v2fm: no visible global function definition for ‘tail’
Undefined global functions or variables:
  coef glm lm na.omit predict predict.glm tail
Consider adding
  importFrom("stats", "coef", "glm", "lm", "na.omit", "predict",
             "predict.glm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘impute’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘default5.eps’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘quick-usage-guide-to-the-fastglm-package.Rmd’
basis_hica: no visible global function definition for ‘princomp’
energy_hica: no visible global function definition for ‘dev.new’
energy_hica: no visible global function definition for ‘points’
energy_hica: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
Package suggested but not available for checking: ‘coxKM’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'FBNormalization.Rd':
  \usage lines wider than 90 characters:
             normDataFileName = NULL, debugFlag = FALSE, plotFlag = FALSE, plotAndSaveFlag = FALSE)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for ‘kmeans’
fcd.start: no visible global function definition for ‘ginv’
fcd.start: no visible global function definition for ‘glmnet’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
mis.cluster: no visible global function definition for ‘permn’
spectral.clustering: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new pnorm
Consider adding
  importFrom("graphics", "abline")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘vert.txt’
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par poisson predict
  qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par", "rug",
             "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘felp.Rmd’ using rmarkdown
File ../../../doc/html/prism.js not found in resource path
Error: processing vignette ‘felp.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘felp.Rmd’

SUMMARY: processing the following file failed:
  ‘felp.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for ‘dmvnorm’
dmymvt: no visible global function definition for ‘dmvt’
gof.test: no visible global function definition for ‘quantile’
gof.test : ecdf: no visible global function definition for ‘mecdf’
gof.test: no visible global function definition for ‘jacobian’
gof.test: no visible global function definition for ‘var’
gradCdfT: no visible global function definition for ‘dt’
gradCdfT: no visible global function definition for ‘pt’
gradCdfT: no visible global function definition for ‘pmvt’
influFun: no visible global function definition for ‘jacobian’
mult.sim: no visible global function definition for ‘rnorm’
plackettFormula: no visible global function definition for ‘pt’
plackettFormula: no visible global function definition for ‘pmvt’
pmymvnorm: no visible global function definition for ‘GenzBretz’
pmymvnorm: no visible global function definition for ‘TVPACK’
pmymvnorm : <anonymous>: no visible global function definition for
  ‘pmvnorm’
pmymvt: no visible global function definition for ‘GenzBretz’
pmymvt: no visible global function definition for ‘TVPACK’
pmymvt : <anonymous>: no visible global function definition for ‘pmvt’
rmymvnorm: no visible global function definition for ‘rmvnorm’
rmymvt: no visible global function definition for ‘rmvt’
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fHMM.Rmd’ using rmarkdown
--- finished re-building ‘fHMM.Rmd’

--- re-building ‘v01_model_definition.Rmd’ using rmarkdown
--- finished re-building ‘v01_model_definition.Rmd’

--- re-building ‘v02_controls.Rmd’ using rmarkdown
File ../../../doc/html/prism.js not found in resource path
Error: processing vignette ‘v02_controls.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v02_controls.Rmd’

--- re-building ‘v03_data_management.Rmd’ using rmarkdown
--- finished re-building ‘v03_data_management.Rmd’

--- re-building ‘v04_model_estimation.Rmd’ using rmarkdown
--- finished re-building ‘v04_model_estimation.Rmd’

--- re-building ‘v05_state_decoding_and_prediction.Rmd’ using rmarkdown
--- finished re-building ‘v05_state_decoding_and_prediction.Rmd’

--- re-building ‘v06_model_checking.Rmd’ using rmarkdown
--- finished re-building ‘v06_model_checking.Rmd’

--- re-building ‘v07_model_selection.Rmd’ using rmarkdown
--- finished re-building ‘v07_model_selection.Rmd’

SUMMARY: processing the following file failed:
  ‘v02_controls.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘MicrobeDS’
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘myTestDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
Missing or unexported object: ‘rules::cubist_rules’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
fishmove : coefs: no visible global function definition for ‘coef’
fishmove : coefs: no visible global function definition for ‘pf’
fishmove: no visible global function definition for ‘lm’
fishmove: no visible global function definition for ‘predict.lm’
fishmove.estimate: no visible global function definition for ‘quantile’
fishmove.estimate : ddoublenorm: no visible global function definition
  for ‘dnorm’
fishmove.query: no visible global function definition for ‘hasArg’
fishmove.query : f: no visible global function definition for ‘pnorm’
fishmove.query: no visible global function definition for ‘uniroot’
pdk: no visible global function definition for ‘hasArg’
pdk : eq: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘leaps’ ‘ltsa’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘bestglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'GetLeapsAR.Rd':
  \usage lines wider than 90 characters:
     GetLeapsAR(z, lag.max = 15, Criterion = "UBIC", Best = 3, Candidates=5, t="default", ExactQ=FALSE)

Rd file 'PlotARSdf.Rd':
  \usage lines wider than 90 characters:
     PlotARSdf(phi = NULL, theta = NULL, units = "radial", logSdf = FALSE, InnovationVariance = 1, main = NULL, sub = NULL, lwd=3, col="blue ... [TRUNCATED]

Rd file 'SelectModel.Rd':
  \usage lines wider than 90 characters:
     SelectModel(z, lag.max = 15, ARModel = c("AR", "ARz", "ARp"), Criterion = "default", Best = 3, Candidates = 5, t="default")

Rd file 'UnitRootTest.Rd':
  \usage lines wider than 90 characters:
     UnitRootTest(z, method = c("MLE", "ExactMLE", "LS", "All"), statistic = c("Z", "T"), NumBoot = 1000, PValueMethod = c("DH", "ET"))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RSvgDevice’
‘library’ or ‘require’ calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘modelfile.dat’ ‘plots’ ‘scorefile.dat’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
RIind: no visible global function definition for ‘aggregate’
RIind: no visible binding for global variable ‘sd’
RIpop: no visible global function definition for ‘aggregate’
RIpop: no visible binding for global variable ‘sd’
SI: no visible global function definition for ‘sd’
SI2: no visible global function definition for ‘sd’
SI3: no visible global function definition for ‘aggregate’
SI3: no visible global function definition for ‘pairs’
SI3: no visible global function definition for ‘cor’
SI4: no visible global function definition for ‘aggregate’
SI4: no visible global function definition for ‘sd’
fCV: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
‘library’ or ‘require’ call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par points predict quantile resid var write.table
Consider adding
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.